ILWS - Charles Sturt University
ILWS - Charles Sturt University

Dr Lee Baumgartner

Dr Lee Baumgartner

Lee Baumgartner is a Freshwater Fish Ecologist who designs, supervises and undertakes into various aspects of the biology and ecology of freshwater fish. His research has been in several broad areas, including fish passage and fish migration, dietary interactions among native fish species, the impact of human disturbance on aquatic ecosystems and, more recently, the effectiveness of native fish stocking. Dr Baumgartners' work has also focused on developing innovative methods for assessment (such as the adaptation of sonar technology to for migration studies) and improving existing fish collection techniques. Much of his work is applied and has fed back into adaptive management strategies which have resulted in state and national policy development. Recently, he has been involved in research activities in the lower Mekong Basin;   specifically understanding mechanisms to help fisheries recover from human disturbance and quantifying the value of fish in a food security context.

Research Interests

  • Freshwater fisheries
  • Fish passage and migration
  • Mitigating human disturbances
  • Hydropower
  • Riverine ecology

Bachelor of Science. (Biological Science) – Deakin University

Bachelor of Science. (Aquatic Science with Honours) – Deakin University

PhD Applied Ecology – University of Canberra

External Appointments & Memberships

Australian Society for Fish Biology (NSW Representative);

American Fisheries Society (member);

Association of Power Biologists (member); Fish Passage Task Force (member);

Murray Cod Fishery Management Group (member);

International Energy Agency Fish and Hydropower Annexe (member);

IUCN Freshwater Fish Specialists Group (member); North East Catchment Management Authority(board member)

NSW Environmental Trust Aquatic Sub-Committee (member);

International Conference on River Connectivity (Chair);

Scientific Panel into Darling River fish deaths (member)

Editorial roles on journals

Marine & Freshwater Research (Associate Editor).

Selected Publications

Peer Reviewed Papers

Baumgartner, L.J., Barlow, C., Mallen-Cooper, M., Boys, C., Marsden, T., Thorncraft, G., Phonekhampheng, O., Singhanouvong, D., Rice, W., Roy, M., Crase, L. & Cooper, B. (2018) Achieving fish passage outcomes at irrigation infrastructure; a case study from the Lower Mekong Basin. Developments in Aquaculture and Fisheries Science. 1-12.

Thiem, J. D., Wooden, I. J., Baumgartner, L. J., Butler, G. L., Forbes, J., Taylor, M. D., & Watts, R. J. (2018) Abiotic drivers of activity in a large, free-ranging, freshwater teleost, Murray cod (Maccullochella peelii). PLOS ONE, 13(6), e0198972

Rourke, M.L., Robinson, W., Baumgartner, L.J.,  Doyle, J., Growns, I., Thiem, J.D. (2018) Sequential fishways reconnect a coastal river reflecting restored migratory pathways for an entire fish community. Restoration Ecology. DOI:10.1111/rec.12886

Conallin, J., Campbell, J. & Baumgartner, L. (2018) Using Strategic Adaptive Management to Facilitate Implementation of Environmental Flow Programs in Complex Social-Ecological Systems. Environmental Management.

Thiem, J. D., Wooden, I. J., Baumgartner, L. J., Butler, G. L., Forbes, J., Taylor, M. D., & Watts, R. J. (2018) Abiotic drivers of activity in a large, free-ranging, freshwater teleost, Murray cod (Maccullochella peelii). PLOS ONE, 13(6), e0198972

Baumgartner, L.J. & Wibowo, A. (2018) Addressing fish passage issues at hydropower and irrigation infrastructure projects in Indonesia. Marine and Freshwater Research Special Issue on Fish and Hydropower. 1-9.

Colotelo, A., Muller, R., Harnish, R., Martinez, J., Phommavong, T., Phommachanh, K., Thorncraft, G., Baumgartner, L.J., Hubbard, J., Rhode, B., Deng, Z. (2018) Injury and mortality of two Mekong species to turbulent shear forces. Marine and Freshwater Research. 1-9.

Silva, L.G.M., Baumgartner, L., Deng, Z.D., Fjeldstad, H-P. (2018) Hydropower development and fish management: a food–water–energy nexus requiring international and multidisciplinary approach. Marine and Freshwater Research, 69: i-iii. DOI: 10.1071/MFv69n12_ED.

Baumgartner, L. J., Boys, C. A., Marsden, T., McPherson, J., Ning, N., Phonekhampheng, O., Robinson, W.A., Sinhanouvong, D., Stuart, I.G., Thorncraft, G. (2018). Comparing fishway designs for application in a large tropical river system. Ecological Engineering, 120, 36-43. doi:

Grieve, B., Baumgartner, L.J., Robinson, W., Silva, L.G.M., Pomorin, K., Thorncraft, G., Ning, N. (2018) Evaluating the placement of PIT tags in tropical river fishes: a case study involving two Mekong River species. Fisheries Research 200: 43-48

Watts, R. J., Kopf, R. K., McCasker, N., Howitt, J. A., Conallin, J., Wooden, I. & Baumgartner, L. (2018) Adaptive Management of Environmental Flows: Using Irrigation Infrastructure to Deliver Environmental Benefits During a Large Hypoxic Blackwater Event in the Southern Murray–Darling Basin, Australia. Environmental Management 61: 469-480 DOI 10.1007/s00267-017-0941-1

Grieve, B., Baumgartner, L.J., Robinson, W., Silva, L., Pomorin, K., Thorncraft, G., Ning, N. (2018) Flexible and non-invasive passive integrated transponder (PIT) tagging protocols for tropical freshwater fish species. MethodX. DOI: 10.1016/j.mex.2018.04.001

Banaduc, D., Voicu, R., Baumgartner, L.J., Maric, S., Dobre, A., Curtean-Banaduc, A. (2017) Technical solutions to mitigate shifting fish fauna zones impacted by long term habitat degradation in the Bistra Mărului River –study case. Transylvanian Review of Systematical and Ecological Research. 20: 75-114. DOI: 10.1515/trser-2018-0006

Silva, A.T., Lucas, M.C., Castro-Santos, T., Katopodis, C., Baumgartner, L.J., Theim, J.D., Pompeu, P.S., O.Brien, G.C., Braun, D.C., Burnett, N.J., Zhu, D.Z., Fjeldstad, HP., Forseth, T., Rajarntnam, N., Williams, J.G., Cooke, S.J. (2017) The future of fish passage science, engineering and practice. Fish and Fisheries DOI: 10.1111/faf.12258

Wilkes, M., Baumgartner, L.J., Pflugrath, B., Boys, C.A., Silva, L.G.M., O’Connor, J., Jones, M., Stuart, I., Habit, E., Link, O., Webb, A.J. (2018) FISH-Net: Probabilistic models for fishway planning, design and monitoring to support environmentally sustainable hydropower in the temperate Southern Hemisphere. Fish and Fisheries. DOI: 10.1111/faf.12282

Millar, J., Robinson, W., Baumgartner, L.J., Chittavong, M., Phommavong, T., Singhanouvong, D. (2018) Local perceptions of changes in the use and management of floodplain fisheries commons: the case of Pak Peung wetland in Lao PDR. Journal of Environment, Development and Sustainability. 1-19;

Baumgartner, L.J., Boys, C.A., Barlow, C., Roy, M. (2017) Lower Mekong Fish Passage Conference: Applying innovation to secure fisheries productivity. Ecological Management and Restoration. 18: 8-12. DOI: 10.1111/emr.12272

Voicu, R., Banaduc, D., Baumgartner, L.J., Voicu, L., Curtean-Banaduc, A. (2017). Upper Caras River (Danube Watershed) fish populations fragmentation – Technical Rehabilitation Proposal. Transylvanian Review of Systematical and Ecological Research. 20: 69-85. DOI: 10.1515/trser-2018-0006

Silva, A.T., Lucas, M.C., Castro-Santos, T., Katopodis, C.,Baumgartner, L.J., Thiem, J.D., Aarestrup, K., Braun, D.,  Burnett, N., Fjeldstad, H.P., Forseth, T., Pompeu, P., Rajaratnam, N., Williams, J., Zhu, D.Z. & Cooke, S.J. (2017) The top five ways to improve global fishway research.Fish and Fisheries. 1-23. DOI: 10.1111/faf.12258.

Kopf, R.K., Nimmo, D.G., Humphries, P., Baumgartner, L., Bode, M., Bond, N., Byrom, A.E., Cucherousset, J., Keller, R.P, King, A.J., McGinness, H., Moyle, P.B., & Olden, J.D. (2017) Confronting the risks of large-scale invasive species control. Nature Ecology and Evolution. (1) 0172, 1-4.

Baumgartner, L.J., Thorncraft, G., Boys, C., Singhanouvong, D., Phonekhampheng, O. (2017) Effects of fluid shear on Silver shark; Implications for hydropower design. Fisheries Management and Ecology. DOI:10.1111/fme.12213

Jones, M., Beyer, K., Zampatti, B. & Baumgartner, L.J. (2017) Influence of altered light intensity on passage success through a vertical slot fishway: implications for instream structures. Ecology of Freshwater fish. DOI:10.1111/fme.12205

Baumgartner, L.J., Wooden, I., Conallin, J., Robinson, W., Thiem, J.D. (2017) Informing water delivery to sustain native fish communities during a long-term drought: Management recommendations for dryland streams in Southern Australia. Ecohydrology. DOI:10.1002/eco.1820

Thiem, J.D, Wooden, I.J., Baumgartner, L.J., Butler, G.L., Forbes, J.P., Conallin, J. (2017) An assessment of the contribution of stocking to golden perch and Murray cod recovery in hypoxic blackwater affected areas of the Edward-Wakool river system, Australia. Austral Ecology. DOI:10.1111/aec.12424

Thiem, J.D., Wooden, I.J., Baumgartner, L.J., Butler, G.L., Forbes, J. P., Conallin, J. (2016). Recovery from a fish kill in a semi-arid Australian river: Can stocking augment natural recruitment processes? Austral Ecology. doi:10.1111/aec.12424.

Cameron, L. Baumgartner, L., Butler, G., Bucher, D. & Lou, D. (2016) Using otolith microchemistry to differentiate between stocked and unstocked Australian bass (Percalates novemaculeata). Fisheries Research, 183:86-91

Harris, J.H., Kingsford, R.T., Peirson, W. & Baumgartner, L.J. (2016) Mitigating the effects of barriers to freshwater fish migrations: the Australian experience. Marine and Freshwater Research.

Forbes, J., Watts, R.J.,  Robinson, W.A., Baumgartner, L.J., Allen, M.S.,  McGuffie, P., Cameron, L.M. & Crook, D.A. (2015) System-Specific Variability in Murray Cod and Golden Perch Maturation and Growth Influences Fisheries Management Options, North American Journal of Fisheries Management, 35:6, 1226-1238, DOI: 10.1080/02755947.2015.1094153

Crook, D.A., O'Mahony, D.J, Gillanders, B.M., Munro, A.R., Sanger, A.C., Thurstan, S., Baumgartner, L.J. (2015). Effects of stocking on the population structure and abundance of a native riverine fish. Marine and Freshwater Research. DO10.1071.MF15037.

Forbes, J., Baumgartner, L.J., Robinson, W., Watts, R.J., McGuffie, P., Cameron, L. and Crook D. (2015). Assessment of stocking effectiveness for Murray cod (Maccullochella peelii) and golden perch (Macquaria ambigua) in rivers and impoundments of south eastern Australia. Marine and Freshwater Research. DOI 10.1071.MF15230

Baumgartner, L.J. (2015). Adaptive management in action: using chemical marking to advance fish recovery programs in the Murray–Darling Basin. Marine and Freshwater Research. DOI10.1071. MF15353.

Boys, C.A., Robinson, W.R., Miller, B., Pflugrath, B., Baumgartner, L.J, Navarro, A., Brown, R. (2015). Understanding fish welfare at river infrastructure: A piecewise regression approach to determining barotrauma injury thresholds. Journal of Fish Biology.

Forbes, J., Baumgartner L.J., Robinson R, Watts R., Murphy, J., Steffe, A. (2015). Recreational Fishing Effort, Catch, and Harvest for Murray cod Maccullochella peelii and Golden perch Macquaria ambigua, in the Murrumbidgee River, Australia.North American Journal of Fisheries Management 35: 254-264.

Brown, R.S., Colotelo, A.H., Pflugrath, B.D., Boys, C.A., Baumgartner, L.J., Deng, Z. D., Silva, L.G.M., Brauner, C.J., Mallen-Cooper, M., Phonekhampeng, O., Thorncraft, G., Singhanouvong, D. (2014). Understanding barotrauma in fish passing hydro and irrigation structures: a global strategy for sustainable development of water resources. Fisheries. 39 (3): 108-122.

Baumgartner, L.J, Zampatti, B., Jones, M., Stuart, I., Mallen-Cooper, M. (2014). Fishways and Fish Migration in the Murray-Darling Basin: Not just an upstream battle. Ecological Management and Restoration, 15 (S1): 28-39.

Baumgartner, L.J., Conallin, J., Wooden, I., Campbell, B., Gee, R. and Robinson, W. (2014). Linking biological needs with hydrology to develop environmental flow requirements for freshwater fish in riverine systems. Fish and Fisheries, 15 (3): 410-427.


Gregory, R., Funge-Smith, S.J. & Baumgartner, L. (2018) An ecosystem approach to promote the integration and coexistence of fisheries within irrigation systems. FAO Fisheries and Aquaculture Circular No.1169. FAO, Rome. Licence: CC BY‐NC‐SA 3.0 IGO.

Silva, L,G., Pearce, L., Mabon, S., Horta, A., Duffy, D., Kopf, S., Ning, N., & Baumgartner, L,J. (2018). Macca’s in the Mannus, Macquarie perch refuge in the Upper Murray. ILWS Report No 114.

Pearce L., Silva, L.G., Mabon, S., Horta, A., Duffy, D., Ning, N., & Baumgartner, L.J. (2018). Finding forgotten fishes, the search for two endangered species in the NSW Murray Catchment. ILWS Report No 112.

Silva, L.G.M., Bell, K., Baumgartner, L.J. (2018) Clean-up procedures applied to global fish kill events: A review for the National Carp Control Plan. FRDC Project No 2016/158. 61pp.

Forbes, J., Steffe, A.S, Baumgartner, L.J. (2017). Preliminary assessment of the Lake Eucumbene summer recreational fishery. New South Wales Department of Primary Industries. Fisheries Final Report No. 156. Sydney, Australia. 38pp.

Baumgartner, L.J., Boys, C.A., Gilligan, D.M., Silva, L.G., Pflugrath, B., Ning, N. (2017) Fish transfer risk associated with Snowy 2.0 pumped hydro scheme. ILWS Report No 107.

Cresswell, I., Baumgartner, L.J., Bond, N., Brown, P., Chua, S., Cooling, M., Cuddy, S., Hillman, T., Kingsford, R., Lester, R., Mallen-Cooper, M., McGinness H, Nicol S, Nielsen D, Robson B, Stratford D, Webb A. (2017). Scoping the development of a method to assess the relative environmental benefits of Complementary Measures. CSIRO Land and Water, Report to the Murray-Darling Basin Commission. 121pp.

Baumgartner, L.J. & Pomorin, K. (2017) The FishNet Database. Institute for Land, Water and Society, Thurgoona. Report to the Australian National Data Service. 6pp.

Baumgartner, L.J. (2017) Peer review of Sustainable Diversion Limit (SDL) adjustment – Complimentary Measures. Institute for Land Water and Society, Thurgoona. Report to Department of Agriculture and Water Resources. 16pp.

Baumgartner, L.J. (2016). Restoring fish migration. RipRap 39:30-32.

Baumgartner, L., Marsden,T., Millar,J., Thorncraft,G., Phonekhampheng, O., Singhanouvong, D., Homsombath, K., Robinson, W., McPherson, J., Martin, K., & Boys, C. (2016) Development of fish passage technology to increase fisheries production on floodplains in the lower Mekong basin, Final Report, ACIAR

Book Chapters

Rice, B. & Baumgartner, L.J. (2018) Sharing international knowledge of fish passage in the Lower Mekong. In Brink, K., Gough, P., Royte, J. Schollema, P.P. & Wanningen, H. From Sea to Source 2.0. Protection and Restoration of fish migration in rivers worldwide. World Fish Migration Foundation. Pp70-75 For a download of the book you will need to sign up for your own download link as this link is only valid for one download.

Pittock, J., Baumgartner, L., Finlayson, C.M., Thiem, J.D., Forbes, J.P., Silva, L.G.M. & Arthington, A.H. (2017) Managing threats to freshwater systems within protected areas in Finlayson, C.M., Arthington, A.H., Pittock, J. (eds) Freshwater Ecosystems in Protected Areas, Conservation and Management.  Routledge

Conference Presentations and Proceedings

Baumgartner, L. (2018) Reducing slope improves small fish passage through a Denil fishway, Presented at the Fish Passage International Conference on River Connectivity, Albury NSW, December 10-14.

Baumgartner, L., Boys, C., Marsden, T., McPherson, J., Ning, N., Phonekhampheng, O., Robinson, W., Singhanouvong, D., Stuart, I., Thorncraft, G. (2018) A cautionary tale about the inhibitory effects of gaged culverts on fish passage restoration efforts, Presented at the Fish Passage International Conference on River Connectivity, Albury NSW, December 10-14.

VuVi A., Baumgartner, L., Cowx, I., Mallen-Cooper, M., Howitt, J., Robinson, W. (2018) Using otoliths to quantify diadromy in the Lower Mekong Basin, Presented at the Fish Passage International Conference on River Connectivity, Albury NSW, December 10-14.

Baumgartner, L.J., Grieve, B., Robinson, W., Silva, L.G.M., Pomorin, K., Thorncraft, G., Ning, N. (2018) Evaluating the placement of PIT tags in tropical river fishes: a case study involving two Mekong River species, Presented at the  Fish Passage International Conference on River Connectivity, Albury NSW, December 10-14.

Conallin, J., Lunn, Z., Baumgartner, L.J., Thein, H., Chan, N. (2018) The importance of determining and maintaining migration corridors for the Hilsa Shad fishery in Myanmar Inland Rivers, Presented at the Fish Passage International Conference on River Connectivity, Albury NSW, December 10-14.

Millar, J., Baumgartner, L., Robinson, W., Homsombath, K. (2018) Listening to local knowledge to inform fish passage and fisheries management, Presented at the Fish Passage International Conference on River Connectivity, Albury NSW, December 10-14.

Mallen-Cooper, M., Baumgartner, L., Stuart, I., Zampatti, B. (2018) The challenge of passing small and large fish in rivers with highly variable hydrology, Presented at the Fish Passage International Conference on River Connectivity, Albury NSW, December 10-14.

Millar, J., Baumgartner, L., Homsoumbath, K., Phommavong, T. (2017) Changes in the role and management of wetland commons in the Lao PDR: the case of Pak Peung wetland. International Association for Society and the Commons Conference 10-15 July 2016, Utrecht, the Netherlands.

Baumgartner, L.  (2016) Designing fishways for floodplain species of the Lower Mekong Basin. Presented at the Australian Society of Fish Biology and Oceania Chondrlchthyan Society Conference 2016, Sept 4-7, Tasmania

Current Projects

PIT tag data analysis project.  Huang, X., Baumgartner, L., and Li, J.(2018-2019) Karltek Pty Ltd., $25,000

Assessing fisheries mitigation measures at Xayaburi Dam in Lao PDR. Baumgartner, L. & Silva, L. (2017-2019) ACIAR, $320,000 (MOU – Xayaburi Power Company Limited)

Developing design guidelines for diversion screens that save native fish and enhance agricultural productivity. Baumgartner, L., Ning, N. & Silva, L. (2018-2020) Ian Potter Foundation, $299,331 Project details

Environmentally sustainable irrigation solutions for the Murray-Darling Basin. (2017) Baumgartner, L.  Australian Academy of Technology and Engineering-Global Connections Fund – Bridging Grant, $49,966

Fish investigations associated with Snowy 2.0 - Snowy Hydro Ltd. (Assignment 1). Baumgartner, L., Silva, L., Ning, N.  (2017-2020) Snowy Hydro Ltd. $61,647 Project details

Fishing for answers: Unlocking spawning secrets of Australian native fish. Baumgartner, L., Silva, L., Thiem, J. (2016-2020) Recreational Fishing Trust. $100,000 Project Details

Macca's in the Mannus, Macquarie Perch Refuge in the Upper Murray. Baumgartner, L., Silva, L., Kopf, S. (2017) NSW Department of Primary Industries/Murray LLS, $120,000 Project details

In search of the elusive Mekong salmon. Baumgartner, L. & Vu, V.A. (PhD student), (2016-2018), National Geographic Society Research Grant, $30,080 Project details

Predicting redfin survival through the Snowy 2.0 scheme. Assignment 2. Baumgartner, L., Silva, L., Ning, N. & McPherson, J. (2018-2019) Snowy Hydro Ltd. $848,803

Quantifying improved fisheries productivity at fish passage rehabilitation sites in Lao PDR. Baumgartner,L., Robinson,W.,  McPherson,J.  with Thorncraft,G. (National University of Laos), Phonekhampheng,O. (National University of Laos),  Singhanouvong,D. (Living Aquatic Resources Research Centre) and Cooper,B. (UniSA) (2016-2020) ACIAR, $1,890,224 Project details

Quantifying improved fisheries productivity at fish rehabilitation sites in Lao PDR extension. Baumgartner, L., Marsden, T., Ning, N. & Horta, A. (2018-2019) ACIAR & USAID, $800,000

Recovery of native fish communities in the Murray-Darling Basin. Baumgartner, L. (2017) Fisheries Research and Development Corporation, $18,948

The role that Deltas play in sustain basin-scale fisheries in the Mekong and Irrawaddy Rivers. Baumgartner L., & Vu. V.A. (PhD student) (2017-2020) IHE Delft. $30,127 Project details

Completed Projects

Development of strategies to optimise release and clean up strategies underpinning possible use of herpes virus 3 (CyHV-3) for carp biocontrol in Australia. Silva, L, & Baumgartner, L. (2017) Fisheries Research & Development Corporation. $39,000

Murray Small-bodied threatened fish project. Baumgartner, L., Silva, L. & Kopf, S. (2017) NSW Department of Primary Industries/Murray LLS, $52,000 Project details

Acoustic Doppler Current Profiler (ADCP) for water research. (2016) Watts, R., Baumgartner, L., Wassens, S., Hall, A. CSU RIBG Grant, $49,919

Complementary measures for native fish. Baumgartner, L. (2017) CSIRO/Murray-Darling Basin Authority. $33,000

Determining optimal design criteria for hydroelectric facilities in NSW and the Lower Mekong Basin. Boys, C.A., Baumgartner, L., Jones, M. (2012-2017) Australian Centre for Renewable Energy, Australian Centre for International Agricultural Research $790,000

Evidence-based scientific advice – Lasting environmental benefits of non-flow measures in the Murray Darling Basin. (2016) Baumgartner, L. Department of Agriculture & Water Resources (Fisheries & Forestry) $9090

Foundational activities for the Fish Theme of Environmental Water Knowledge and Research (EWKR). Baumgartner, L. (2016) MDRFC, $16,800

Recovery of native fish communities in the Murray-Darling Basin. Baumgartner, L. (2017) Fisheries Research and Development Corporation, $18,948.

Measuring Impacts of Lower Mekong Basin fish passage. Baumgartner, L. (2015) Australian Centre for International Agricultural Research. $1.84 M

Modelling the success of Australian Bass re-stocking. Suthers, Taylor, Baumgartner, L. (2008-2011) Australian Research Council. $210,000

Murray River Fishway Assessment Project. Baumgartner, L., Zampatti, B., Jones, M. (2002-2013) Murray Darling Basin. $5.8M

Transferring fish passage technology to the Lower Mekong and Murray-Darling Basins. Baumgartner, L. (2007-2015) Australian Centre for International Agricultural Research $1.83M