Summary

CSIRO AquaWatch mission has officially launched on the World Water Day on March 22nd, 2023. The mission will provide near-real-time updates and predictive forecasting for water quality, which will support better water quality management and early warning of harmful events.  Read the media release here.

Aims

My part in the CSIRO AquaWatch mission is the Water Quality Modelling project, which is to develop a predictive model for water quality parameters such as Temperature, Stratification, TSS, Turbidity, DO, and to forecast algae bloom events in lake and river systems as follows (by 2026):

• Deliver modelled baseline water quality maps.

• Develop core modelling tools: integrated hydrodynamic and biogeochemical models to model water quality.

• Use the hybrid modelling system (AI/ML + process-based) to ​develop a short-term (5-7 days) forecast tool.

• Analyse high-frequency physics, chemical, and biological water quality data.

• Combine other remote sensing data, such as hyperspectral reflectance, to improve monitoring and forecasting modelling capabilities.

• Assess the social and economic benefits of water quality forecasting.

• Use a hybrid modelling (Physics informed neural networks (PINNs)) approach for water security.

•  Work with the Digital Water and Landscape program to develop a national fish kill index.

• Support the needs of pilot projects, especially leading the international pilots in Vietnam.

Papers and reports from this project (first- or co-author):

Journal papers:

• Nguyen, D., Biswas, T., Anstee, J., Ford, P. W., & Joehnk, K. (2025). Managing Cyanobacteria Blooms in Lake Hume: Abundance Dynamics Across Varying Water Levels. Water, 17(6), 891. https://doi.org/10.3390/w17060891  

• Nguyen, D., Kirkpatrick, M. P., Williamson, N., Armfield, S. W. & Lin, W. (2023), Influences of channel sinuosity on flow and boundary shear stress in thermally stratified turbulent open-channel bends. Journal of Hydraulic Engineering 149(9), 04023029. DOI: https://doi.org/10.1061/JHEND8.HYENG-13396

Submitted journal papers:

• Duy Nguyen, Tim J. Malthus, Janet Anstee, Tapas Biswas, Erin Kenna, and Klaus Joehnk (2025). Forecasting cyanobacteria cell counts in lakes based on hyperspectral sensing. Remote Sensing (Submitted).

• Duy Nguyen, Klaus Joehnk, Tapas Biswas, Janet Anstee, Phillip Ford (2025). Managing Cyanobacteria Blooms in Lake Hume: Impacts of Inflows and Risk Minimisation. Water (Submitted).

• Yiqing Guo, Duy Nguyen, Klaus Joehnk (2025). Cloud-Gao Filling for Satellite-Derived River Water Quality Data with Time-Series Foundation Models. IEEE Geoscience and Remote Sensing Letters (Drafted)

• Leyde Briceno Medina, Duy Nguyen, Klaus Joehnk, Ravinesh C. Deo, Mumtaz Ali, Salvin Prasad, Nathan Downs (2025). Predicting Non-mixing River Flow Using a Data-driven Approach: A Case Study in Menindee Region in Australia. Science of The Total Environment (Drafted)

• Warren Jin, Amelia Genova, Joel J. Dabrowski, Yiqing Guo, Luis Riera Garcia, Duy Nguyen, Klaus Joehnk, Peter Toscas (2025). Advancing Dissolved Oxygen Forecasting with Uncertainty: Long-Term High-Frequency Predictions for Australian Rivers. Engineering Applications of Artificial Intelligence (drafted).

Technical Reports:

• Biswas TK, Nguyen D, Romas E, Bhogal D, Tzimas A, Tursunalieva A, Malthus T, Zhao Y and Joehnk KD (2025). Development of an integrated water quality monitoring and forecasting system for Grahamstown Dam and Williams River. CSIRO Project No.C034709. Final report to the Hunter Water Corporation. pp 92. CSIRO Environment and Data61, Canberra, ACT 2601 Australia.

• Joehnk, K.D., Anstee, J., Ford, P., … Nguyen, D, et al. (2025). Development of improved cyanobacteria remote sensing capability and forecasting model for Melbourne Water Western Treatment Plant’s lagoon systems (L25W and L55E) - Stage II project. Report prepared for Melbourne Water Corporation by CSIRO Environment, Australia.

• Biswas TK, Nguyen D, Bhogal D, Kenna E, Malthus T, Carlin G, Davies M and Joehnk KD (2024). AquaWatch Inland Water Quality Pilot: Application of Earth Observation and Modelling for Forecasting of Inland Water Quality (Lake Hume and Lake Tuggeranong). A technical report to the SmartSat CRC Pty Ltd. pp 52. EP2024-3024. CSIRO Environment, Canberra, ACT 2601 Australia.

Conference Proceedings:

• Nguyen, Duy; Joehnk, Klaus; Biswas, Tapas. Forecasting lakes cyanobacteria blooms using in-situ hyperspectral observations. In: Advancing Earth Observation Forum 2024; 10 to end of 12 Sep 2024; Adelaide, Australia. csiro; 2024. 1. csiro:EP2024-2192. http://hdl.handle.net/102.100.100/637783?index=1

• Nguyen, Duy; Joehnk, Klaus; Biswas, Tapas. Managing Cyanobacteria Blooms in Lake Hume by Changing its Hydrodynamics. In: ASLO 2024 Meeting: Adapting to a Changing World; 02 to end of 07 Jun 2024; Madison, Wisconsin, USA. csiro; 2024. 1. csiro:EP2024-0798. http://hdl.handle.net/102.100.100/635739?index=1

• Nguyen, Duy; Kirkpatrick, Michael P. ; Joehnk, Klaus; Biswas, Tapas. Modelling thermal stratification, overturning and mixing in Australian Rivers. In: Freshwater Science 2023; 03 to end of 07 Jun 2023; Brisbane, Australia. csiro; 2023. 1p. csiro:EP2023-0287. http://hdl.handle.net/102.100.100/486843?index=1

Currently working:

• Climate model outputs impact on stratification and cyanobacteria modeling. (first author, in preparation, will be drafted by July 2025).

• 1D chained modeling of cyanobacteria in a pond system. (first author, in preparation, will be drafted by Sept 2025).

• Physics-Informed Neural Networks for 2D thermal stratified lake. (co-author, in preparation).

• Time series water quality forecast using Foundation models for the Murray-Darling Basin. (co-author, in preparation).

• Time series water quality forecast using Foundation models for aquaculture farms in Vietnam. (co-PI, in preparation).

• Reena Kapoor, Yanchang Zhao, Devesh Bhogal, Duy Nguyen, Peter Toscas, and Klaus Joehnk (2025). Water Stratification Modeling with Bayesian Networks. (co-author, in preparation).

• Jean-Michel Perraud et al (2025). Air2stream over the Murray-Darling Basin: Predict River Surface Temperature Using Air Temperature. (co-author, in preparation).

• Warren Jin et al. (2025). Thermal Stratification Forecasting Using Deep Learning Approach. (co-author, in preparation).

• Klaus Joehnk and Peter Toscas et al. (2025). A Systematic Review of Water Quality Modeling. (co-author, in preparation).

Designing the AquaWatch's Science Application Traceability Matrix (SATM): Duy is a member of a working group to develop a matrix that offered a structured pathway from overarching objectives down to eventual publications, encompassing mission objectives, science objectives, measurement requirements, instrument specifications, and system requirements for the AquaWatch mission. The team’s efforts have resulted in the organization of goals, objectives, and impacts into a cohesive tracking tool that guides mission planning and facilitates solution delivery. This comprehensive chart addresses parameter management, cascading down to instrument design, model requirements, data products, and the desires of end-users.

• Arnold Dekker, Isabel Fratter, Tarun Saunders, Joshua Pease, Duy Nguyen, Klaus Joehnk, Dar Tisham, Andrew Prata, Hannelie Botha, Tim Malthus, Janet Anstee, Tim Bolton, Gemma Kerrisk, Timon Sotiropoulos, Rob Woodcock, Flora Kerblat, Zandria Farrell. Benefits of a Science and Applications Traceability Matrix (SATM) for Water Quality Integrating Measurements from In-Situ and Earth Observation Sensors, as Well as Including Predictive Water Quality Modelling. In Proceedings of Living Planet Symposium 2025, Vienna, Austria, p. 3452, B.02.09, 23-27 June 2025.

Summary

In the hot, drought-prone climate,  thermal stratification is common in Australia's rivers.  The presence of thermal stratification prevents mixing between the surface and bottom water, leading to the formation and persistence of oxygen stratification which in turn can produce reducing conditions at depth, releasing contaminants from bottom sediments and increasing concentrations of dissolved ammonia, hydrogen sulfide, iron, manganese and phosphorus. Such conditions can make the bottom waters unsuitable for benthic organisms and fish.  Persistent thermal stratification has also been identified as one of the major risk factors for toxic cyanobacteria outbreaks. 

Fluid flows through a bend lead to strong lateral secondary circulations. Those circulations lead to asymmetric spatial distributions of turbulent mixing,  and significantly affect the distribution of both mean velocity and turbulent shear stress within the river.  Those factors can have significant effects on thermal stratification.

Aims

A motivation for this study is to make progress towards a greater understanding of the effects of meander bends on thermal stratification in rivers. 

• Present detailed numerical data on the turbulent flow in a stratified open-channel meander with heating through the upper surface. 

• Develop simple scaling relations that quantify the effects of meanders on riverine thermal stratification and destratification processes.  

This will enable a more accurate determination of the flow rates required to maintain the health of our river systems.

Approach

The main numerical approaches are direct numerical simulation (DNS) and large eddy simulation (LES) using our in-house code, PUFFIN. These simulations are run on massively parallel high-performance computing facilities, including the University’s HPC facility, Artemis, and the NCI facility, Gadi. 

Outcomes

Below are some figures and movies from recent DNS results.

Video 1: When the river passes through a meandering section, complex secondary currents are formed, which generate upwelling and downwelling zones. These circulations help to mix the river water, allowing the river to 'breathe'. Upwelling can be seen close to the apex, where turbulence from the river bed (visualised here in terms of vorticity) is carried up to the surface on the inside of the bend and then outwards across the surface of the river. These secondary currents lead to the beautiful temperature patterns seen in the right-hand panel.

Video 2: Night-time river flow with surface cooling - late stage. The upper and lower panels show side views of the temperature and vorticity fields. The surface of the river is cooled by convection and radiation to the colder surroundings above. Over time the cool, dense surface water forms plumes that plunge downwards, breaking down the stable stratification. This allows mixing through the full depth of the water body, which refreshes the river, reoxygenating the deep waters and restoring water quality. This video shows the final stages with the temperature field rescaled to show the plumes more clearly. 

Figure 1: Contours of the depth-averaged streamwise velocity when varying channel curvature.

Figure 2: Contours of the depth-averaged vertical vorticity when varying channel sinuosity.

Publications

Summary

Sea Spray droplets and marine aerosols have significant roles in Earth's weather and climate. In the air-sea boundary layer, sea-spray take part in a series of complex transport processes, including the transfer of mass, momentum, energy, and humidity. A common method for determining spray production at the ocean surface is to measure an airborne concentration and infer a surface flux; however, there remain large uncertainty in sea spray droplet and aerosol generation functions due to a lack of insight into the turbulent transport of droplets in the vicinity of surface waves. This project aims to study the mechanisms that control the transport of sea spray in the turbulent flow over a moving wave in a wave tank tunnel, and to evaluate the influence of waves on the concentration profile of sea spray droplets, to investigate droplet trajectories and dynamics over a range of droplet sizes

Approach

We use a large eddy simulation (LES) model with Lagrangian droplet tracking to study particle transport over a moving wavy surface by looking specifically at their average concentration profiles.

Outcomes

• While all the parameters: the Stokes number, the dimensionless settling velocity and wave, profoundly influence the concentration profiles, the settling velocity gives the most effect. 

• Different inertia particles interact selectively with near-wall turbulent flows structures, producing different distributions at specific regions on the wave surface.

Publications

1. Nguyen, D. (2017) Sea Spray Concentration Profile in the Marine Atmospheric Boundary Layer. Available at: https://curate.nd.edu/show/pc289g57z8s.

This is a proposed project which was submitted to the Aus4Innovation program. It is a collaboration between The Fluid Dynamics Research Group at the University of Sydney and The Vietnam Academy of Water Resources. It successfully went to the second round but lost to the final shortlist. It has never got funded and has stayed on the shelf since. I hope publishing it here might attract ideas, collaborations, and fundings to make the project alive.  

Statement

Climate change and human modifications of river flows are leading to significant changes in the Cua Sot estuary, Ha Tinh Province, Vietnam (location attached above). Climate change is altering the nature of the atmospheric system, leading to significant changes to rainfall and runoff distribution in Vietnam. Rainfall is projected to increase in intensity and frequency, but its distribution will be mainly in the wet season. Meanwhile, rainfall in the dry season is predicted to decrease. Associated with prolonged hot and dry periods, these conditions exacerbate the low flow rate in the dry season in Vietnamese river systems. In addition, economic development activities demand ever-increasing water consumption to meet the expansion of production, especially in the agricultural sector. Thus, the combination of climate change, sea-level rise, expansion of production and livelihood activities have added great threats and challenges to coastal countries, including Vietnam, which has been categorized among the countries most affected by climate change. These adverse effects are already apparent in Vietnam’s coastal estuaries during the dry period when the water discharge rate from upstream is low. Under these conditions, the tidally driven salinity intrusion is extending further inland, increasing the salinity contaminated area and leading to adverse effects on socio-economic development, especially in the agricultural sector.

Aims

The main aim of this study is to explore inland salinity intrusion in coastal estuarine areas of Vietnam.

1. Establish a physical experimental model for an estuary area

2. Conduct experiments to identify salinity intrusion boundaries with different scenarios of flow conditions and tides (including sea-level rise)

3. Build a mathematical model to simulate the salinity intrusion process and test with real measured data. 

The expected results of the joint research will be a prerequisite for scaling up and applying to other similar areas. 

Approaches

• Establish a large-scale physical model (approx. 25 x 25 m) of the estuary, namely a two-phase model (salinity-freshwater): The upper boundary is the upstream flow, the lower boundary is the tidal variation at the estuary. On the physical model, the formation and characteristics of saltwater will be observed according to the change of upstream flow and the tidal characteristic (amplitude - cycle) at the estuary along with the topography characteristics of the river bed. A case study is an estuary in Cua Sot, Nghen River in Ha Tinh province (Figure 1). Figure 2 shows the large-scale physical model developed for the previous study (now it has been demolished)

• Build a mathematical model: Improving the open-source model (1D model) developed by Australian experts to build a simulation model and calibrate model parameters from experimental results derived from physical models.

• Develop the application of salinity propagation in practice through the development of a salinity intrusion map for the selected estuary.

The large-scale model of Cua Sot Estuary in Vietnam Academy of Water Resources Lab

Innovation

The proposed research collaboration will be the first-ever experimental study on a physical model on the salinity intrusion problem in Vietnam.

Readiness
Several approaches and solutions have been developed in the past for the individual system components as described in available literature. This research is innovative in the sense that it looks for solutions regarding the spatial scale at which experiments are available for salinity intrusion modelling. The fundamental research on salinity intrusion has been successfully implemented in USyd, so it is ready to be scaled up. The techniques, although they will be tested for Vietnam, have the potential to be more widely applicable to other coastal regions in the world. Thus, the research collaboration project demonstrates readiness and viability.

Summary

Rolling waves on the spillway can significantly complicate the operation of the hydro-power plant. The design of waterworks spillways is often limited to the calculation for a uniform and uneven flow regime, without considering issues of waves and aeration. The turbulence created by those rapid waves reduces the stability and reliability of the structure. It is important to check the possibility of wave formation in an aerated stream on an open spillway. The calculation is based on the building of an open spillway for the complex hydroelectric on Dam'Bri River, Lam Dong province, which is located 140km northeast of Ho Chi Minh city, the south of Vietnam.

Approach

We used the recommendations for the hydraulic calculation of culverts of gravity spillways for aeration and wave formation by B.E. Vedeneev for the real spillway construction in Vietnam.  (Рекомендации по гидравлическому расчету водопропускных трактов безнапорных водосбросов на аэрацию и волнообразование. П 66-77/ВНИИГ им. Б.Е. Веденеева. – Л., 1978. – 51 с).

Outcomes

The length of the Dam'Bri dam is not enough for the formation of rolling waves,   anti-wave measures at the spillway were not required. 

There is a formation of aeration and cavitation at high-speed discharge. It is necessary to increase the dam headroom and the sidewalls of the spillway by the size of the aeration layer. 

Publications

1. Duy Nguyen, Thien Luu, Lavrov Nikolai. The stability of rapid flow at idle unconfined spillway hydro power plant Dam'Bri, Vietnam; "The ecological state of the environment, scientific and practical aspects of modern hydraulic technologies, #6, Ryazan: Ryazan State Argo-technological University, 265 – 271, 2013 paper (In Russian)