Ulm, Sean, Mcniven, Ian J., Summerhayes, Glenn R., Wu, Pei-hua, Bunbury, Magdalena M.E., Petchey, Fiona, Hua, Quan, Skelly, Robert, Lambrides, Ariana B.J., Rowe, Cassandra, Lowe, Kelsey M., Reepmeyer, Christian H., Maclaurin, Cailey, Woo, Katherine G.P., Harris, Matthew, Morgan, Sarah B., Turner-Kose, Kayla L., Slater, Sarah A., Connelly, Joshua D., Kneppers, Michael C., Szabó, Katherine, Fairbairn, Andrew, Haberle, Simon G., Hopf, Felicitas, Bultitude, Robert, Ash, Jeremy, Lewis, Stephen E., Beaman, Robin J., Leon, Javier Xavier, McDowell, Matthew C., Potter, Martin, Connelly, Benjamin, Little, Chris, Jackson, Scott, McCarthy, John, Nothdurft, Luke D., Zhao, Jian-xin, Bird, Michael I., Felgate, Matthew W., Cobus, Brian, and Walmbaar Aboriginal Corporation RNTBC, (2024) Early Aboriginal pottery production and offshore island occupation on Jiigurru (Lizard Island group), Great Barrier Reef, Australia. Quaternary Science Reviews. 108624. (In Press)

Lewis, Stephen, McCloskey, Gillian, Bainbridge, Zoe, Davis, Aaron, Bartley, Rebecca, and Turner, Ryan (2023) Sediment and nutrient flux from land. In: Wolanski, Eric, and Kingsford, Michael J., (eds.) Oceanographic Processes of Coral Reefs: Physical and Biological Links in the Great Barrier Reef. CRC Press, Boca Raton, FL, USA. (In Press)

Zhang, Jingyi, Yu, Wusheng, Lewis, Stephen, Thompson, Lonnie G, Bowen, Gabriel J, Yoshimura, Kei, Werner, Martin, Chakraborty, Supriyo, Jing, Zhaowei, Ma, Yaoming, Guo, Xiaoyu, Xu, Baiqing, Wu, Guangjian, Guo, Rong, Qu, Dongmei, and Cauquoin, Alexandre (2023) Controls on Stable Water Isotopes in Monsoonal Precipitation Across the Bay of Bengal: Atmosphere and Surface Analysis. Geophysical Research Letters, 50 (5). e2022GL102229.

Li, Yao, Yu, Wusheng, Tian, Lide, Lewis, Stephen, Yoshimura, Kei, Weng, Cheng, Cui, Jiangpeng, Ma, Yaoming, Guo, Rong, Zhang, Jingyi, Jing, Zhaowei, Shao, Lili, Guo, Ziaoyu, and Wang, Yong (2023) Diagnosis of atmospheric circulation shifts in the central Tibetan Plateau: Evidence from stable isotopes. Atmospheric Research, 282. 106536.

Silburn, D. Mark, Fillols, Emilie, Rojas-Ponce, Samuel, Lewis, Steve, and McHugh, A.D. (2023) Direct comparison of runoff of residual and knockdown herbicides in sugarcane using a rainfall simulator finds large difference in runoff losses and toxicity relative to diuron. Science of the Total Environment, 863. 160976.

Burrows, Ryan M., Garzon-Garcia, Alexandra, Burton, Joanne, Lewis, Stephen E., Gruber, Renee K., Brodie, Jon E., and Burford, Michele A. (2023) Factors affecting broadscale variation in nearshore water-column organic carbon concentrations along the Great Barrier Reef. Regional Studies in Marine Science, 63. 103032.

Bainbridge, Zoe, Olley, Jon, Wilkinson, Scott, Bartley, Rebecca, Lewis, Stephen, Dougall, Cameron, Khan, Sana, Kuhnert, Petra, and Burton, Joanne (2023) Refining fine sediment source identification through integration of spatial modelling, concentration monitoring and source tracing: A case study in the Great Barrier Reef catchments. Science of the Total Environment, 10. 164731.

Lewis, S., James, C., and Bainbridge, Z. (2023) Water quality signatures of pristine and near-pristine landscapes in the Great Barrier Reef Catchment Area. Report. TropWATER, James Cook University, Townsville, QLD, Australia.

Ani, Chinenye J., Smithers, Scott G., Lewis, Stephen, Baird, Mark, and Robson, Barbara (2023) eReefs modelling suggests Trichodesmium may be a major nitrogen source in the Great Barrier Reef. Estuarine, Coastal and Shelf Science, 285. 108306.

Bahadori, Mohammad, Chen, Chengrong, Lewis, Stephen, Wang, Juntao, Shen, Jupei, Hou, Enqing, Rezaei Rashti, Mehran, Huang, Qiaoyun, Bainbridge, Zoe, and Stevens, Tom (2023) The origin of suspended particulate matter in the Great Barrier Reef. Nature Communications, 14. 5629.

Jing, Zhaowei, Yu, Wusheng, Lewis, Stephen, Thompson, Lonnie G., Xu, Jie, Zhang, Jingyi, Xu, Baiqing, Wu, Guangjian, Ma, Yaoming, Wang, Yong, and Guo, Rong (2022) Inverse altitude effect disputes the theoretical foundation of stable isotope paleoaltimetry. Nature Communications, 13. 4371.

Robson, Barbara, Lewis, Stephen, Kroon, Frederieke, Fabricius, Katharina, Warne, Michael, and Wolanski, Eric (2022) Jon Brodie Memorial: The sources, fates and consequences of pollutants in tropical shelf systems. Marine Pollution Bulletin, 179. 113669.

Moran, D., Robson, B., Gruber, R., Waterhouse, J., Logan, M., Petus, C., Howley, C., Lewis, S., Tracey, D., James, C., Mellors, J., Bove, U., Davidson, J., Glasson, K., Lefevre, C., Macadam, A., Shanahan, M., Vasile, R., Zagorskis, I., and Shellberg, J. (2022) Marine Monitoring Program: Annual Report for Inshore Water Quality Monitoring 2020-2021. Report. Great Barrier Reef Marine Park Authority, Townsville, QLD, Australia.

Lloyd-Jones, Luke R., Kuhnert, Petra M., Lawrence, Emma, Lewis, Stephen E., Waterhouse, Jane, Gruber, Renee K., and Kroon, Frederieke J. (2022) Sampling re-design increases power to detect change in the Great Barrier Reef’s inshore water quality. PLoS ONE, 17 (7). e0271930.

Bahadori, Mohammad, Wang, Jun-Tao, Shen, Ju-pei, Lewis, Stephen, Rezaei Rashti, Mehran, and Chen, Chengrong (2022) Soil organic matter and geochemical characteristics shape microbial community composition and structure across different land uses in an Australian wet tropical catchment. Land Degradation and Development, 33 (6). pp. 817-831.

Comeros-Raynal, Mia T., Brodie, Jon, Bainbridge, Zoe, Choat, John Howard, Curtis, Meagan, Lewis, Stephen, Stevens, Thomas, Shuler, Christopher K., Sudek, Mareike, and Hoey, Andrew S. (2021) Catchment to sea connection: impacts of terrestrial run-off on benthic ecosystems in American Samoa. Marine Pollution Bulletin, 169. 112530.

Lambert, Victoria, Bainbridge, Zoe T., Collier, Catherine, Lewis, Stephen E., Adams, Matthew P., Carter, Alex, Saunders, Megan I., Brodie, Jon, Turner, Ryan D.R., Rasheed, Michael A., and O'Brien, Katherine R. (2021) Connecting targets for catchment sediment loads to ecological outcomes for seagrass using multiple lines of evidence. Marine Pollution Bulletin, 169. 112494.

Zhang, Jingyi, Yu, Wusheng, Jing, Zhaowei, Lewis, Stephen, Xu, Baiqing, Ma, Yaoming, Wei, Feili, Luo, Lun, and Qu, Dongmei (2021) Coupled effects of moisture transport pathway and convection on stable isotopes in precipitation across the East Asian Monsoon Region: implications for paleoclimate reconstruction. Journal of Climate, 34 (24). pp. 9811-9822.

Jing, Zhaowei, Yu, Wusheng, Schneider, Andreas, Borsdorff, Tobias, Landgraf, Jochen, Lewis, Stephen, Zhang, Jingyi, Tang, Wenjun, Ma, Yaoming, Xu, Baiqing, and Qu, Dongmei (2021) Interannual variation in stable isotopes in water vapor over the Northern Tibetan Plateau Linked to ENSO. Geophysical Research Letters, 48 (8). e2021GL092708.

Lewis, Stephen E., Bartley, Rebecca, Wilkinson, Scott, Bainbridge, Zoe T., Kinsey-Henderson, Anne, James, Cassandra S., Irvine, Scott A., and Brodie, Jon E. (2021) Land use change in the river basins of the Great Barrier Reef, 1860 to 2019: a foundation for understanding environmental history across the catchment to reef continuum. Marine Pollution Bulletin, 166. p. 112193.

Bainbridge, Zoe, Lewis, Stephen, Stevens, Thomas, Petus, Caroline, Lazarus, Emily, Gorman, Jessica, and Smithers, Scott (2021) Measuring sediment grain size across the catchment to reef continuum: improved methods and environmental insights. Marine Pollution Bulletin, 168. 112339.

Lewis, S., and Bainbridge, Z. (2021) Much more than just sediments: The importance of sediment composition for Great Barrier Reef ecosystems. Report. Reef and Rainforest Research Centre, James Cook University, Cairns, QLD, Australia.

Bahadori, Mohammad, Chen, Chengrong, Lewis, Stephen, Boyd, Sue, Rashti, Mehran, Esfandbod, Maryam, Van Zwieten, Lukas, and Kuzyakov, Yakov (2021) Soil organic matter formation is controlled by the chemistry and bioavailability of organic carbon inputs across different land uses. Science of the Total Environment, 770. 145307.

Saha, Narottam, Webb, Gregory E., Zhao, Jian-Xin, Lewis, Stephen E., Nguyen, Ai Duc, and Feng, Yuexing (2021) Spatiotemporal variation of rare earth elements from river to reef continuum aids monitoring of terrigenous sources in the Great Barrier Reef. Geochimica et Cosmochimica Acta, 299. pp. 85-112.

Canto, Marites M., Fabricius, Katharina E., Logan, Murray, Lewis, Stephen, McKinna, Lachlan I.W., and Robson, Barbara J. (2021) A benthic light index of water quality in the Great Barrier Reef, Australia. Marine Pollution Bulletin, 169. 112539.

Garzon-Garcia, Alexandra, Burton, Joanne M., Lewis, Stephen, Bainbridge, Zoe, De Hayr, Rob, Moody, Philip, and Brodie, Jon (2021) The bioavailability of nitrogen associated with sediment in riverine plumes of the Great Barrier Reef. Marine Pollution Bulletin, 173. 112910.

Lewis, S., Bainbridge, Z., and Smithers, S. (2021) A synthesis of the changing sources, transport and delivery of sand to the Burdekin River Delta: implications for the stability of the Bowling Green spit: A Report for Water Planning Ecology, Science and Technology Division, Department of Environment and Science. Report. TropWATER, James Cook University, Townsville, QLD, Australia.

Fillols, Emilie, Davis, Aaron M., Lewis, Stephen E., and Ward, Andrew (2020) Combining weed efficacy, economics and environmental considerations for improved herbicide management in the Great Barrier Reef catchment area. Science of the Total Environment, 720. 137481.

Lambert, V., Collier, C., Brodie, J., Adams, M.P., Baird, M., Bainbridge, Z., Carter, A., Lewis, S., Rasheed, M., Saunders, M., and O'Brien, K. (2020) Connecting Sediment Load Targets to Ecological Outcomes for Seagrass. Report. Reef and Rainforest Research Centre, Cairns, QLD, Australia.

Bahadori, Mohammad, Chen, Chengrong, Lewis, Stephen, Rashti, Mehran Rezaei, Cook, Freeman, Parnell, Andrew, Esfandbod, Maryam, and Stevens, Thomas (2020) Tracing the sources of sediment and associated particulate nitrogen from different land uses in the Johnstone River catchment, Wet Tropics, northeastern Australia. Marine Pollution Bulletin, 157. 111344.

Lewis, S., Bainbridge, Z., Stevens, T., Garzon-George, A., Bahador, M., Burton, J., Rezaei Rasht, M., James, C., Smithers, S., and Olley, J. (2020) What’s really damaging the Reef?: Tracing the origin and fate of the ecologically detrimental sediment and associated bioavailable nutrients. Report. Reef and Rainforest Research Centre, Cairns, QLD, Australia.

Saha, Narottam, Webb, Gregory E., Zhao, Jian-xin, Nguyen, Ai Duc, Lewis, Stephen, and Lough, Janice (2019) Coral-based high-resolution rare earth element proxy for terrestrial sediment discharge affecting coastal seawater quality, Great Barrier Reef. Geochimica et Cosmochimica Acta, 254. pp. 173-191.

Petus, Caroline, Waterhouse, Jane, Lewis, Stephen, Vacher, Michael, Tracey, Dieter, and Devlin, Michelle (2019) A flood of information: using Sentinel-3 water colour products to assure continuity in the monitoring of water quality trends in the Great Barrier Reef (Australia). Journal of Environmental Management, 248. 109255.

Bahadori, Mohammad, Chen, Chengrong, Lewis, Stephen, Rashti, Mehran Rezaei, Cook, Freeman, Parnell, Andrew, Esfandbod, Maryam, and Boyd, Sue (2019) A novel approach of combining isotopic and geochemical signatures to differentiate the sources of sediments and particulate nutrients from different land uses. Science of the Total Environment, 655. pp. 129-140.

Wolff, Nicholas H., Da Silva, Eduardo Teixeira, Devlin, Michelle, Anthony, Kenneth R.N., Lewis, Stephen, Tonin, Hemerson, Brinkman, Richard, and Mumby, Peter J. (2018) Contribution of individual rivers to Great Barrier Reef nitrogen exposure with implications for management prioritization. Marine Pollution Bulletin, 133. pp. 30-43.

Kuhnert, P.M., Pagendam, D.E., Bartley, R., Gladish, D.W., Lewis, S.E., and Bainbridge, Z.T. (2018) Making management decisions in the face of uncertainty: a case study using the Burdekin catchment in the Great Barrier Reef. Marine and Freshwater Research, 69 (8). pp. 1187-1200.

Ulm, Sean, Williams, Alan N., Turney, Chris, and Lewis, Stephen (2018) Australia's coastal living is at risk from sea level rise, but it's happened before. The Conversation, 16 January 2018.

Petus, Caroline, Devlin, Michelle, da Silva, Eduardo Teixeira, Lewis, Stephen, Waterhouse, Jane, Wenger, Amelia, Bainbridge, Zoe, and Tracey, Dieter (2018) Defining wet season water quality target concentrations for ecosystem conservation using empirical light attenuation models: a case study in the Great Barrier Reef (Australia). Journal of Environmental Management, 213. pp. 1-16.

Fillols, E., Lewis, S., and Davis, A. (2018) Efficacy and environmental runoff impact of alternative pre-emergent herbicides to diuron applied on trash blanketed ratoons. In: Proceedings of the 40th Annual Conference of the Australian Society of Sugar Cane Technologists (40) pp. 281-292. From: ASSCT 2018: 40th Annual Conference of the Australian Society of Sugar Cane Technologists, 17-20 April 2018, Mackay, QLD, Australia.

Bainbridge, Z., Lewis, S., Bartley, R., Fabricius, K., Collier, C., Waterhouse, J., Garzon-Garcia, A., Robson, B., Burton, J., Wenger, A., and Brodie, J. (2018) Fine sediment and particulate organic matter: a review and case study on ridge-to-reef transport, transformations, fates, and impacts on marine ecosystems. Marine Pollution Bulletin, 135. pp. 1205-1220.

Ryan, E.J., Smithers, S.G., Lewis, S.E., Clark, T.R., Zhao, J.-X., and Hua, Q. (2018) Fringing reef growth over a shallow last interglacial reef foundation at a mid-shelf high island: Holbourne Island, central Great Barrier Reef. Marine Geology, 398. pp. 137-150.

Ortiz, Juan-Carlos, Wolff, Nicholas H., Anthony, Kenneth R.N., Devlin, Michelle, Lewis, Stephen, and Mumby, Peter J. (2018) Impaired recovery of the Great Barrier Reef under cumulative stress. Science Advances, 4 (7). eaar6127. pp. 1-8.

Williams, Alan N., Ulm, Sean, Sapienza, Tom, Lewis, Stephen, and Turney, Chris S.M. (2018) Sea-level change and demography during the last glacial termination and early Holocene across the Australian continent. Quaternary Science Reviews, 182. pp. 144-154.

Lewis, S., Bainbridge, Z., Stevens, T., Garzon-Garcia, A., Chen, C., Burton, J., Bahadon, M., Rezaei Rashti, M., Gorman, J., Smithers, S., Olley, J., Moody, P., and Dehayr, R. (2018) Sediment tracing from the catchment to reef 2016 to 2018: Flood plume, marine sediment trap and logger data time series. Report. Reef and Rainforest Research Centre, Cairns, QLD, Australia.

Novic, Andrew Joseph, Ort, Christopher, O'Brien, Dominique S., Lewis, Stephen E., Davis, Aaron M., and Mueller, Jochen F. (2018) Understanding the uncertainty of estimating herbicide and nutrient mass loads in a flood event with guidance on estimator selection. Water Research, 132. pp. 99-110.

Cooper, Michelle, Lewis, Stephen E., Stieglitz, Thomas C., and Smithers, Scott G. (2018) Variability of the useful life of reservoirs in tropical locations: a case study from the Burdekin Falls Dam, Australia. International Journal of Sediment Research, 33. pp. 93-106.

Lewis, Stephen E., Lough, Janice M., Cantin, Neal E., Matson, Eric G., Kinsley, Les, Bainbridge, Zoe T., and Brodie, Jon E. (2018) A critical evaluation of coral Ba/Ca, Mn/Ca and Y/Ca ratios as indicators of terrestrial input: new data from the Great Barrier Reef, Australia. Geochimica et Cosmochimica Acta, 237. pp. 131-154.

Ryan, Emma J., Smithers, Scott G., Lewis, Stephen E., Clark, Tara R., and Zhao, Jian-xin (2018) The variable influences of sea level, sedimentation and exposure on Holocene reef development over a cross-shelf transect, central Great Barrier Reef. Diversity, 10 (4). 110. pp. 1-17.

Bartley, Rebecca, Waters, David, Turner, Ryan, Kroon, Frederieke, Garzon-Garcia, Alex, Kuhnert, Petra, Lewis, Stephen, Smith, Rachel, Bainbridge, Zoe, Olley, Jon, Brooks, Andrew, Burton, Jo, Brodie, Jon, and Waterhouse, Jane (2017) 2017 Scientific Consensus Statement: land use impacts on the Great Barrier Reef water quality and ecosystem condition, Chapter 2: sources of sediment, nutrients, pesticides and other pollutants to the Great Barrier Reef. Report Section. State of Queensland.

Eberhard, Rachel, Thorburn, Peter, Rolfe, John, Taylor, Bruce, Ronan, Mike, Webber, Tony, Flint, Nicole, Kroon, Frederieke, Silburn, Mark, Bartley, Rebecca, Davis, Aaron, Wilkinson, Scott, Lewis, Stephen, Star, Megan, Poggio, Mark, Windle, Jill, Marshall, Nadine, Hill, Rosemary, Maclean, Kirsten, Lyons, Pethie, Robinson, Cathy, Adame, Fernanda, Selles, Amelia, Griffiths, Matthew, Gunn, John, and McCosker, Kevin (2017) 2017 Scientific Consensus Statement: land use impacts on the Great Barrier Reef water quality and ecosystem condition. Chapter 4: management options and their effectiveness. Report Section. State of Queensland.

Waters, D.K., and Lewis, S.E. (2017) Calculating sediment trapping efficiency for reservoirs in series. In: Proceedings of the 22nd International Congress on Modelling and Simulation. pp. 1990-1996. From: MODSIM 2017: 22nd International Congress on Modelling and Simulation, 3-8 December 2017, Hobart, TAS, Australia.

Novic, Andrew Joseph, O'Brien, Dominique S., Kaserzon, Sarit L., Hawker, Darryl W., Lewis, Stephen E., and Mueller, Jochen F. (2017) Monitoring herbicide concentrations and loads during a flood event: a comparison of grab sampling with passive sampling. Environmental Science and Technology, 51 (7). pp. 3880-3891.

Brodie, Jon, Devlin, Michelle, and Lewis, Stephen (2017) Potential enhanced survivorship of crown of thorns starfish larvae due to near-annual nutrient enrichment during secondary outbreaks on the central mid-shelf of the Great Barrier Reef, Australia. Diversity, 9 (17).

Brodie, Jon E., Lewis, Stephen E., Collier, Catherine J., Wooldridge, Scott, Bainbridge, Zoe, Waterhouse, Jane, Rasheed, Michael, Honchin, Carol, Holmes, Glen, and Fabricius, Katharina (2017) Setting ecologically relevant targets for river pollutant loads to meet marine water quality requirements for the Great Barrier Reef, Australia: a preliminary methodology and analysis. Ocean & Coastal Management, 143. pp. 136-147.

Cooper, Michelle, Lewis, Stephen E., and Smithers, Scott G. (2017) Spatial and temporal dynamics of suspended sediment causing persistent turbidity in a large reservoir: Lake Dalrymple, Queensland, Australia. Marine and Freshwater Research, 68 (7). pp. 1377-1390.

Waterhouse, Jane, Brodie, Jon, Lewis, Stephen, and Audas, Donna-Marie (2016) Land-sea connectivity, ecohydrology and holistic management of the Great Barrier Reef and its catchments: time for a change. Ecohydrology and Hydrobiology, 16 (1). pp. 45-57.

Gladish, Daniel W., Kuhnert, Petra M., Pagendam, Daniel E., Wikle, Christopher K., Bartley, Rebecca, Searle, Ross D., Ellis, Robin J., Dougall, Cameron, Turner, Ryan D.R., Lewis, Stephen E., Bainbridge, Zoe T., and Brodie, Jon E. (2016) Spatio-temporal assimilation of modelled catchment loads with monitoring data in the Great Barrier Reef. Annals of Applied Statistics, 10 (3). pp. 1590-1618.

Ryan, E.J., Smithers, S.G., Lewis, S.E., Clark, T.R., and Zhao, J.X. (2016) The influence of sea level and cyclones on Holocene reef flat development: Middle Island, central Great Barrier Reef. Coral Reefs, 35 (3). pp. 805-818.

Chaiechi, Taha, Stoeckl, Natalie, Jarvis, Diane, Lewis, Stephen, and Brodie, Jon (2016) Assessing the impact of price changes and extreme climatic events on sediment loads in a large river catchment near the Great Barrier Reef. Australian Journal of Agricultural and Resource Economics, 60 (3). pp. 386-405.

Lewis, Stephen E., Silburn, D. Mark, Kookana, Rai S., and Shaw, Melanie (2016) Pesticide behavior, fate, and effects in the Tropics: an overview of the current state of knowledge. Journal of Agricultural and Food Chemistry, 64 (20). pp. 3917-3924.

Furuichi, Takahisa, Olley, Jon, Wilkinson, Scott, Lewis, Stephen, Bainbridge, Zoe, and Burton, Joanne (2016) Paired geochemical tracing and load monitoring analysis for identifying sediment sources in a large catchment draining into the Great Barrier Reef Lagoon. Geomorphology, 266. pp. 41-52.

Fabricius, K.E., Logan, M., Weeks, S.J., Lewis, S.E., and Brodie, J. (2016) Changes in water clarity in response to river discharges on the Great Barrier Reef continental shelf: 2002-2013. Estuarine, Coastal and Shelf Science, 173. A1-A15.

O'Brien, Dominique, Lewis, Stephen, Davis, Aaron, Gallen, Christie, Smith, Rachael, Turner, Ryan, Warne, Michael, Turner, Scott, Caswell, Stewart, Mueller, Jochen F., and Brodie, Jon (2016) Spatial and temporal variability in pesticide exposure downstream of a heavily irrigated cropping area: application of different monitoring techniques. Journal of Agricultural and Food Chemistry, 64 (20). 5b04710. pp. 3975-3989.

Ryan, E.J., Smithers, S.G., Lewis, S.E., Clark, T.R., and Zhao, J.X. (2016) Chronostratigraphy of Bramston Reef reveals a long-term record of fringing reef growth under muddy conditions in the central Great Barrier Reef. Palaeogeography, Palaeoclimatology, Palaeoecology, 441 (Part 4). pp. 734-747.

Bainbridge, Zoe, Lewis, Stephen, Smithers, Scott, Wilkinson, Scott, Douglas, Grant, Hillier, Stephen, and Brodie, Jon (2016) Clay mineral source tracing and characterisation of Burdekin River (NE Australia) and flood plume fine sediment. Journal of Soils and Sediments, 16 (2). pp. 687-706.

Ryan, Emma, Lewis, Stephen E., Smithers, Scott G., Clark, Tara R., and Zhao, Jian-xin (2016) Multi-scale records of reef development and condition provide context for contemporary changes on inshore reefs. Global and Planetary Change, 146. pp. 162-178.

Melland, Alice R., Silburn, D. Mark, McHugh, Allen D., Fillols, Emilie, Rojas-Ponce, Samuel, Baillie, Craig, and Lewis, Stephen (2016) Spot spraying reduces herbicide concentrations in runoff. Journal of Agricultural and Food Chemistry, 60 (20). pp. 4009-4020.

Lewis, Stephen E., Wüst, Raphael A.J., Webster, Jody, M., Collins, John, Wright, Shelley, A., and Jacobsen, Geraldine (2015) Rapid relative sea-level fall along north-eastern Australia between 1200 and 800 cal. yr BP: an appraisal of the oyster evidence. Marine Geology, 370. pp. 20-30.

Lough, J.M., Lewis, S.E., and Cantin, N.E. (2015) Freshwater impacts in the central Great Barrier Reef: 1648–2011. Coral Reefs, 34 (3). pp. 739-751.

Brodie, Jon, Lewis, Stephen, Davis, Aaron, Bainbridge, Zoe, O'Brien, Dominique, Waterhouse, Jane, Devlin, Michelle, and Thomas, Colette R. (2015) Management of agriculture to preserve environmental values of the Great Barrier Reef, Australia. In: Chicharo, Luís, Müller, Felix, and Fohrer, Nicola, (eds.) Ecosystems Services and River Basin Ecohydrology. Springer, Dordrecht, Netherlands, pp. 275-292.

Delandmeter, Philippe, Lewis, Stephen E., Lambrechts, Jonathan, Deleersnijder, Eric, Legat, Vincent, and Wolanski, Eric (2015) The transport and fate of riverine fine sediment exported to a semi-open system. Estuarine, Coastal and Shelf Science , 167 (Part B). pp. 336-346.

Stoeckl, Natalie, Farr, Marina, Jarvis, Diane, Larson, Silva, Esparon, Michelle, Sakata, Hana, Chaiechi, Taha, Liu, Hongbo, Brodie, Jon, Lewis, Stephen, Mustika, Putu, Adams, Vanessa, Chacon, Adriana, Bos, Melissa, Pressey, Bob, Kubiszewski, Ida, and Costanza, Bob (2014) The Great Barrier Reef World Heritage Area: its 'value' to residents and tourists, and the effect of world prices on it. Final report to the National Environmental Research Program. Report. Reef and Rainforest Research Centre, James Cook University, Cairns, QLD, Australia.

Bainbridge, Zöe T., Lewis, Stephen E., Smithers, Scott G., Kuhnert, Petra M., Henderson, Brent L., and Brodie, Jon E. (2014) Fine-suspended sediment and water budgets for a large, seasonally dry tropical catchment: Burdekin River catchment, Queensland, Australia. Water Resources Research, 50 (11). pp. 9067-9087.

Davis, A.M., Lewis, S.E., Brodie, J.E., and Benson, Ash (2014) The potential benefits of herbicide regulation: a cautionary note for the Great Barrier Reef catchment area. Science of the Total Environment, 490. pp. 81-92.

Yu, Wusheng, Yao, Tandong, Lewis, Stephen, Tian, Lide, Ma, Yaoming, Xu, Baiqing, and Qu, Dongmei (2014) Stable oxygen isotope differences between the areas to the north and south of Qinling Mountains in China reveal different moisture sources. International Journal of Climatology, 34 (6). pp. 1760-1772.

Bartley, Rebecca, Bainbridge, Zoe T., Lewis, Stephen E., Kroon, Frederieke J., Wilkinson, Scott N., Brodie, Jon E., and Silburn, D. Mark (2014) Relating sediment impacts on coral reefs to watershed sources, processes and management: a review. Science of the Total Environment, 468-469. pp. 1138-1153.

Oliver, Danielle P., Anderson, Jenny S., Davis, Aaron, Lewis, Stephen, Brodie, Jon, and Kookana, Rai (2014) Banded applications are highly effective in minimising herbicide migration from furrow-irrigated sugar cane. Science of the Total Environment, 466-467. pp. 841-848.

Lewis, Stephen E., Olley, Jon, Furuichi, Takahisa, Sharma, Ashneel, and Burton, Joanne (2014) Complex sediment deposition history on a wide continental shelf: implications for the calculation of accumulation rates on the Great Barrier Reef. Earth and Planetary Science Letters, 393 (1). pp. 146-158.

Lough, J.M., Llewellyn, L.E., Lewis, S.E., Turney, C.S.M., Palmer, J.G., Cook, C.G., and Hogg, A.G. (2014) Evidence for suppressed mid-Holocene northeastern Australian monsoon variability from coral luminescence. Paleoceanography, 29 (6). pp. 581-594.

Bartley, Rebecca, Bainbridge, Zoe T., Lewis, Stephen E., Kroon, Frederieke J., Wilkinson, Scott N., Brodie, Jon E., and Silburn, Mark D. (2014) From coral to cows: using ecosystem processes to inform catchment management of the Great Barrier Reef. In: Proceedings of the 7th Australian Stream Management Conference. pp. 9-16. From: 7th Australian Stream Management Conference: catchment to coast, 27-30 July 2014, Townsville, QLD, Australia.

Davis, Aaron M., Lewis, Stephen E., O'Brien, Dominique S., Bainbridge, Zoë T., Bentley, Christie, Mueller, Jochen F., and Brodie, Jon E. (2014) Water resource development and high value coastal wetlands on the lower Burdekin floodplain, Australia. In: Wolanski, Eric, (ed.) Estuaries of Australia in 2050 and Beyond. Estuaries of the World . Springer, Dordrecht, The Netherlands, pp. 223-246.

Davis, A.M., Thorburn, P.J., Lewis, S.E., Bainbridge, Z.T., Attard, S.J., Milla, R., and Brodie, J.E. (2013) Environmental impacts of irrigated sugarcane production: Herbicide run-off dynamics from farms and associated drainage systems. Agriculture, Ecosystems and Environment, 180. pp. 123-135.

McKenna, S.A., Rasheed, M.A., Lewis, S.E., Tol, S.J., and Sankey, T. (2013) Abbot Point proposed dredge disposal areas: benthic habitat survey: 2013. Report. TropWATER, James Cook University, Cairns, QLD, Australia.

Mallela, Jennie, Lewis, Stephen E., and Croke, Barry (2013) Coral skeletons provide historical evidence of phosphorus runoff on the Great Barrier Reef. PLoS ONE, 8 (9). e75663. pp. 1-10.

Reeves, Jessica M., Bostock, Helen C., Ayliffe, Linda K. , Barrows, Timothy T., De Deckker, Patrick, Devriendt, Laurent S., Dunbar, Gavin B., Drysdale, Russell N., Fitzsimmons, Kathryn E., Gagan, Michael K., Griffiths, Michael L., Haberle, Simon G., Jansen, John D., Krause, Claire, Lewis, Stephen, McGregor, Helen V. , Mooney, Scott D., Moss, Patrick, Nanson, Gerald C., Purcell, Anthony, and van der Kaars, Sander (2013) Palaeoenvironmental change in tropical Australasia over the last 30,000 years: a synthesis by the OZ-INTIMATE group. Quaternary Science Reviews, 74. pp. 97-114.

Lewis, Stephen E., Sloss, Craig R., Murray-Wallace, Colin V., Woodroffe, Colin D., and Smithers, Scott G. (2013) Post-glacial sea-level changes around the Australian margin: a review. Quaternary Science Reviews, 74. pp. 115-138.

Lewis, Stephen E., Bainbridge, Zöe T., Kuhnert, Petra M., Sherman, Bradford S., Henderson, Brent, Dougall, Cameron, Cooper, Michelle, and Brodie, Jon E. (2013) Calculating sediment trapping efficiencies for reservoirs in tropical settings: a case study from the Burdekin Falls Dam, NE Australia. Water Resources Research, 49 (2). pp. 1017-1029.

Brodie, Jon, Waterhouse, Jane, Maynard, Jeffrey, Bennett, John, Furnas, Miles, Devlin, Michelle, Lewis, Stephen, Collier, Catherine, Schaffelke, Britta, Fabricius, Katharina, Petus, Caroline, da Silva, Eduardo, Zeh, Daniel, Randall, Lucy, Brando, Vittorio, McKenzie, Len, O'Brien, Dominique, Smith, Rachael, Warne, Michael, Brinkman, Richard, Tonin, Hemerson, Bainbridge, Zoe, Bartley, Rebecca, Negri, Andrew, Turner, Ryan, Davis, Aaron, Bentley, Christie, Mueller, Jochen, Alvarez-Romero, Jorge, Henry, Nyssa, Waters, David, Yorkston, Hugh, and Tracey, Dieter (2013) Assessment of the relative risk of water quality to ecosystems of the Great Barrier Reef. A report to the Department of the Environment and Heritage Protection, Queensland Government, Brisbane - Report 13/28. Report. James Cook University, Townsville, QLD, Australia.

Lewis, Stephen E., Wust, Raphael A.J., Webster, Jody M., Shields, Graham A., Renema, Willem, Lough, Janice M., and Jacobsen, Geraldine (2012) Development of an inshore fringing coral reef using textural, compositional and stratigraphic data from Magnetic Island, Great Barrier Reef, Australia. Marine Geology, 299-302. pp. 18-32.

Lewis, Stephen E., Schaffelke, Britta, Shaw, Melanie, Bainbridge, Zoë T., Rohde, Ken W., Kennedy, Karen, Davis, Aaron M., Masters, Bronwyn L., Devlin, Michelle J., Mueller, Jochen F., and Brodie, Jon E. (2012) Assessing the additive risks of PSII herbicide exposure to the Great Barrier Reef. Marine Pollution Bulletin, 65 (4-9). pp. 280-291.

Davis, Aaron M., Lewis, Stephen E., Bainbridge, Zoë T., Glendenning, Lionel, Turner, Ryan D.R., and Brodie, Jon E. (2012) Dynamics of herbicide transport and partitioning under event flow conditions in the lower Burdekin region, Australia. Marine Pollution Bulletin, 65 (4-9). pp. 182-193.

Bainbridge, Zoe T., Wolanski, Eric, Alvarez Romero, Jorge, Lewis, Stephen E., and Brodie, Jon E. (2012) Fine sediment and nutrient dynamics related to particle size and floc formation in a Burdekin River flood plume, Australia. Marine Pollution Bulletin, 65 (4-9). pp. 236-248.

Kennedy, Karen, Schroeder, Thomas, Shaw, Melanie, Haynes, David, Lewis, Stephen, Bentley, Christie, Paxman, Chris, Carter, Steve, Brando, Vittorio E., Bartkow, Michael, Hearn, Laurence, and Mueller, Jochen F. (2012) Long term monitoring of photosystem II herbicides: correlation with remotely sensed freshwater extent to monitor changes in the quality of water entering the Great Barrier Reef, Australia. Marine Pollution Bulletin, 65 (4-9). pp. 292-305.

Waterhouse, J., Brodie, J., Lewis, S., and Mitchell, A. (2012) Quantifying the sources of pollutants in the Great Barrier Reef catchments and the relative risk to reef ecosystems. Marine Pollution Bulletin, 65 (4-9). pp. 394-406.

Kuhnert, Petra M., Henderson, Brent L., Lewis, Stephen E., Bainbridge, Zoe T., Wilkinson, Scott N., and Brodie, Jon E. (2012) Quantifying total suspended sediment export from the Burdekin River catchment using the loads regression estimator tool. Water Resources Research, 48 (4). W04533. pp. 1-18.

Brodie, J.E., Kroon, F.J., Schaffelke, B., Wolanski, E.C., Lewis, S.E., Devlin, M.J., Bohnet, I.C., Bainbridge, Z.T., Waterhouse, J., and Davis, A.M. (2012) Terrestrial pollutant runoff to the Great Barrier Reef: an update of issues, priorities and management responses. Marine Pollution Bulletin, 65 (4-9). pp. 81-100.

Lewis, S.E., Brodie, J.E., McCulloch, M.T., Mallella, J., Jupiter, S.D., Williams, H. Stuart, Lough, J.M., and Matson, E.G. (2012) An assessment of an environmental gradient using coral geochemical records, Whitsunday Islands, Great Barrier Reef, Australia. Marine Pollution Bulletin, 65 (4-9). pp. 306-319.

Brodie, Jon, Wolanski, Eric, Lewis, Stephen, and Bainbridge, Zoe (2012) An assessment of residence times of land-sourced contaminants in the Great Barrier Reef lagoon and the implications for management and reef recovery. Marine Pollution Bulletin, 65 (4-9). pp. 267-279.

Kennedy, Karen, Devlin, Michelle, Bentley, Christie, Lee-Chue, Kristie, Paxman, Chris, Carter, Steve, Lewis, Stephen, Brodie, Jon, Guy, Ellia, Vardy, Suzanne, Martin, Katherine C., Jones, Alison, Packett, Robert, and Mueller, Jochen F. (2012) The influence of a season of extreme wet weather events on exposure of the World Heritage Area Great Barrier Reef to pesticides. Marine Pollution Bulletin, 64 (7). pp. 1495-1507.

Lewis, S.E., Smith, R., Brodie, J.E., Bainbridge, Z.T., Davis, A.M., and Turner, R. (2011) Using monitoring data to model herbicides exported to the Great Barrier Reef, Australia. In: Proceedings of 19th International Congress on Modelling and Simulation. pp. 2051-2056. From: MODSIM 2011 19th International Congress on Modelling and Simulation, 12–16 December 2011, Perth, WA, Australia.

Devlin, Michelle, and Lewis, Stephen (2011) Advancing Our Understanding of the Source, Transport and Impacts of Pesticides on the Great Barrier Reef and in Associated Ecosystems: a review of MTSRF research outputs, 2006-2010. Report. Reef and Rainforest Research Centre, Cairns, QLD.

Bainbridge, Zoe, Dight, Ian, Yorkston, Hugh, Lewis, Stephen, and Brodie, Jon (2011) Catchment management in a dry tropical river near the Great Barrier Reef. In: Wilkinson, Clive, and Brodie, Jon, (eds.) Catchment Management and Coral Reef Convservation. Global Coral Reef Monitoring Network and Reef and Rainforest Research Centre, Townsville, QLD, Australia, pp. 96-97.

Scott, Colin, Lewis, Steve E., Milla, Rob, Taylor, Matthew C., Rodgers, Andrew J.W., Dumsday, Geoff, Brodie, Jon E., Oakeshott, John G., and Russell, Robyn J. (2010) A free-enzyme catalyst for the bioremediation of environmental atrazine contamination. Journal of Environmental Management, 91 (10). pp. 2075-2078.

Lambrechts, J., Humphrey, C., McKinna, L., Gourge, O., Fabricius, K.E., Mehta, A.J., Lewis, S., and Wolanski, E. (2010) Importance of wave-induced bed liquefaction in the fine sediment budget of Cleveland Bay, Great Barrier Reef. Estuarine, Coastal and Shelf Science , 89 (2). pp. 154-162.

Lewis, Stephen Edward, Henderson, Robert A., Dickens, Gerald R., Shields - Zhou, Graham A., and Coxhell, Simon (2010) The geochemistry of primary and weathered oil shale and coquina across the Julia Creek vanadium deposit (Queensland, Australia). Mineralium Deposita, 45 (6). pp. 599-620.

Lewis, Stephen, Milla, Rob, Brodie, Jon, Bainbridge, Zoë, and Davis, Aaron (2009) Pesticide residues in the Great Barrier Reef. Pesticides News, 86. pp. 8-11.

Lewis, Stephen E., Brodie, Jon E., Bainbridge, Zoe T., Rohde, Ken W., Davis, Aaron M., Masters, Bronwyn L., Maughan, Mirjam, Devlin, Michelle J., Mueller, Jochen F., and Schaffelke, Britta (2009) Herbicides: a new threat to the Great Barrier Reef. Environmental Pollution, 157 (8-9). pp. 2470-2484.

Bainbridge, Zoe T., Brodie, Jon E. , Faithful, John W., Sydes, Damon A., and Lewis, Stephen E. (2009) Identifying the land-based sources of suspended sediments, nutrients and pesticides discharged to the Great Barrier Reef from the Tully–Murray Basin, Queensland, Australia. Marine and Freshwater Research, 60 (11). pp. 1081-1090.

Lewis, S.E., Sherman, B.S., Bainbridge, Z.T., Brodie, J.E., and Cooper, M. (2009) Modelling and monitoring the sediment trapping efficiency and sediment dynamics of the Burdekin Falls Dam, Queensland, Australia. In: Proceedings of 18th World IMACS Congress and MODSIM09 International Congress on Modelling and Simulation. pp. 4022-4028. From: 18th World IMACS Congress and MODSIM09 International Congress on Modelling and Simulation, 13–17 July 2009, Cairns, QLD, Australia.

Bainbridge, Z.T., Brodie, J.E., Lewis, S.E., Waterhouse, J., and Wilkinson, S.N. (2009) Utilising catchment modelling as a tool for monitoring Reef Rescue outcomes in the Great Barrier Reef catchment area. In: Proceedings of 18th World IMACS Congress and MODSIM09 International Congress on Modelling and Simulation. pp. 3301-3307. From: 18th World IMACS Congress and MODSIM09 International Congress on Modelling and Simulation, 13–17 July 2009, Cairns, QLD, Australia.

Brodie, Jon, Pearson, Richard, Lewis, Stephen, Bainbridge, Zoe, Waterhouse, Jane, and Prange, Joelle (2009) Water quality research: baseline synthesis and year 1 summary. Report. Reef and Rainforest Research Centre on behalf of the Australian Government's Marine and Tropical Sciences Research Facility, Cairns, Australia.

Brodie, Jon, Lewis, Stephen, Bainbridge, Zoe, Mitchell, Alan, Waterhouse, Jane, and Kroon, Frederieke (2009) Target setting for pollutant discharge management of rivers in the Great Barrier Reef catchment area. Marine and Freshwater Research, 60 (11). pp. 1141-1149.

Davis, Aaron, Lewis, Stephen, Bainbridge, Zoe, Brodie, Jon, and Shannon , Evan (2008) Pesticide residues in waterways of the lower Burdekin region: challenges in ecotoxicological interpretation of monitoring data. Australasian Journal of Ecotoxicology, 14. pp. 89-108.

Bainbridge, Zoe, Brodie, Jon, Manning, Chris, Waterhouse, Jane, Lewis, Stephen, Gooch, Margaret, and Broderick, Kathleen (2008) Integrated Monitoring and Modelling Strategy for the Black Ross Water Quality Improvement Plan. Report. Australian Centre for Tropical Freshwater Research, Townsville, QLD, Australia.

Lewis, Stephen E., Wust, Raphael A.J., Webster, Jody M., and Shields, Graham A. (2008) Mid-late Holocene sea-level variability in eastern Australia. Terra Nova, 20 (1). pp. 74-81.

Brodie, Jon, Bainbridge, Zoe, and Lewis, Stephen (2008) Tully Murray Water Quality Monitory Strategy. Report. Australian Centre for Tropical Freshwater Research, Townsville, QLD, Australia.

Lewis, Stephen E., Shields, Graham A., Kamber, Balz S., and Lough, Janice M. (2007) A multi-trace element coral record of land-use changes in the Burdekin River catchment, NE Australia. Palaeogeography, Palaeoclimatology, Palaeoecology, 246 (2-4). pp. 471-487.

Bainbridge, Z.T., Lewis, S.E., and Brodie, J.E. (2007) Sediment and nutrient exports for the Burdekin River catchment, north Queensland: a comparison of monitoring and modelling data. In: Proceedings of MODSIM07: the International Congress on Modelling and Simulation. pp. 874-880. From: MODSIM07: International Congress on Modelling and Simulation, 10-13 December 2007, Christchurch, New Zealand.

Lewis, S.E., Bainbridge, Z.T., and Brodie, J.E. (2007) A review of load tools available for calculating pollutant exports to the Great Barrier Reef lagoon: a case study of varying catchment areas. In: Proceedings of MODSIM07: the International Congress on Modelling and Simulation. pp. 2396-2402. From: MODSIM07 International Congress on Modelling and Simulation: Land, Water & Environmental Management: Integrated Systems for Sustainability, 10-13 December 2007, Christchurch, New Zealand.

Nagle, Cate, Lewis, Sharon, Meiser, Bettina, Metcalfe, Sylvia, Carlin, John B., Bell, Robin, Gunn, Jane, and Halliday, Jane (2006) Evaluation of a decision aid for prenatal testing of fetal abnormalities: a cluster randomised trial [ISRCTN22532458]. BMC Public Health, 6. 96.

Lewis, Stephen Edward (2005) Environmental trends in the GBR lagoon and Burdekin River catchment during the mid-Holocene and since European settlement using Porites coral records, Magnetic Island, QLD. PhD thesis, James Cook University.