Mount Lofty Ranges (MLR) Water Quality

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Carbon Sequestration Strategy

Project Partners:

SARDI, CSIRO, and The University of Adelaide

Research Theme:



Project Overview

An Improved Water Quality Model for the Onkaparinga Catchment

The Mt Lofty Ranges (MLR) watershed is comprised of a number of catchments consisting of the Torrens and Little Para catchments in the north and the Onkaparinga and Myponga catchments in the south. The focus of this study was the Onkaparinga catchment and contains a number of sub-catchment sites that can export very high nutrient loads during periods of intense runoff. The monitoring sites of interest in this report were chosen during a workshop with SA Water, SA EPA and SARDI for their importance in the catchment under study.

Flow data and water quality data is collected at gauges. Because the composite sampling network was established in 1996, historical data for flow date back further than for water quality. Furthermore, flow is measured at regular intervals (every 5 minutes) and is easily aggregated to obtain measurements of daily flow volumes. Composite water quality sampling results in flow-weighted samples of various constituents that are composited for collection every two to four weeks.

Developing the dSedNet plugin

The catchments of the MLR are a primary source of potable water to Adelaide and its environs. Because the catchments are mixed land uses (e.g. horticulture, grazing, hobby farms), the water exiting the catchments is not pristine and many studies have been undertaken to identify and quantify (through measurement and prediction) the sources of constituents, especially total suspended sediment (TSS), total phosphorus (TP) and total nitrogen (TN). Several models that describe the hydrology and related constituent generation and transport through these sub-catchments have been developed, the most recent using the eWater Source® platform. These studies, and models development, have highlighted constituent modelling as one of the issues requiring further work. It was considered that the Source model, as implemented at that time, predicted TN loads in the MLR quite well at longer timescales – however TP and TSS were generally underestimated in high rainfall years and overestimated in low rainfall years. The Event Mean Concentration (EMC) and Dry Weather Concentrations (DWC) approach used in Source was the major factor contributing to the poor representation of inter-annual variability of flow, due to the limited response to flow inherent in this model structure.

Progress Update and Key Findings

An Improved Water Quality Model for the Onkaparinga Catchment

This component of the research focused on three key pollutants, namely total suspended sediment (TSS), total nitrogen (TN) and total phosphorous (TP). Using statistical models, the processes that drive hydrology and water quality in the Onkaparinga catchment were studied and applied to land-use change scenario modelling. Specifically, this research focused on:

  • Applying a Bayesian calibration approach to calibrate the SIMHYD rainfall-runoff model for use in the Onkaparinga catchment and quantify potential sources of uncertainty in the hydrology
  • Developing statistical models (site based models) for sites monitored in the Onkaparinga catchment in the MLR watershed for the purpose of quantifying constituent loads with an estimation of uncertainty
  • Using statistical models to investigate three scenarios of land-use change and whether there are changes in loads and the uncertainty around loads

Statistical models employed to address the above points, consisted of generalised additive models (GAMs) and generalised additive mixed models (GAMMs) through the Loads Regression Estimator (LRE) package that was developed for the quantification of loads for the Great Barrier Reef catchments (by CSIRO). Site based models for the six sites studied in the Onkaparinga catchment used a variety of hydrological variables as covariates for understanding the variation in the data measured for each site. Specifically, these hydrological variables included flow, decomposed into baseflow and runoff as well as flow discounting terms that took into account past characteristics of the hydrograph. This could consist of a total accumulation of flow from the start of sampling to the short-term flow record prior to the current constituent sampled. Models were fit using the LRE package using the R statistical programming language.

Three scenarios that were explored as part of this research consisted of:

  • Investigating the sale of SA Water land holdings in Scott Creek sub-catchment
  • Quantifying the impact of continued expansion of perennial horticulture in the Cox Creek sub-catchment.
  • Quantifying the impact on water quality of infill within township boundaries of Aldgate Creek Railway Station.

These scenarios were determined at meetings with SA Water and SA EPA and were structured around the statistical modelling approach used to evaluate each scenario. A Random Forests modelling approach was used to develop a spatio-temporal model for each constituent across the six sites of interest in the Onkaparinga catchment. The model is non-parametric and popular in the machine learning and is based on decision tree methodology. The approach can take a large number of potential covariates as predictors to develop an ensemble of decision trees on bootstrap samples of the data. Variable importance rankings can assist in identifying important variables.

Developing the dSedNet plugin

To improve the parameterisation and methods used in Source for modelling constituents, the SedNet dynamic modelling capability was extended. This was primarily a software development exercise, using the Source model already developed for the catchments of the MLR. Three key activities were undertaken:

  • The development of a spatial parameterisation tool to enable the rapid set-up of dSedNet models
  • The development of two component modules of the dSedNet plugin – the hillslope and gully sediment generation models
  • Trialling of the dSedNet plugin in the Onkaparinga catchment (Houlgraves Weir).

The development of the dSedNet plugin and spatial parameterisation tool was the main activity within the project. Testing of the plugin was performed by running a series of small modelling trials. In addition to testing the robustness of the code, these trials provided an opportunity to consider the advantages of the dSedNet approach.

The dSedNet software is being developed as a Source plugin; the spatial parameterisation tool has been developed within the core of Source platform. Plugins are easily distributed between modellers and models, while changes to Source core are more difficult to manage as they require quality assurance by eWater and need to fit in with Source development and release cycles. This is advantageous from a maintenance perspective, but does reduce the control that the project team has over its release. At this point, a release date is unknown. The South Australian project team has a version of Source that contains the spatial parameterisation tool, and the dSedNet plugin, and a training workshop was held in May 2015.

The MLR Source model was modified to use the dSedNet plugin, with some parameters changed to match those used in other studies (such as that by Wilkinson et al. in 2014). This is referred as the baseline, noting that it has not been calibrated against observed water quality data.

Additionally, two calibrations (multi- and single-region) of the rainfall-runoff model (SIMHYD) were used, giving two sets of results. The multi-region simulation used separate SIMHYD parameters for each region, according to the calibration of its gauge. The single-region calibration treated all sub-catchments as a single region, i.e. they all had the same SIMHYD parameters. The need to do this emerged during the trials to more closely match the hydrology to other studies and demonstrates the importance of using good hydrological models for constituent modelling.

The Onkaparinga catchment was chosen for the trials, using observations at Houlgraves Weir. Three trials were conducted against previous studies: (i) SedNet sediment budgets Wilkinson et al. (2005), (ii) existing EMC/DWC Source model, and (iii) statistically derived loads.

Simulations were run for the two rainfall-runoff calibrations (multi- and single-region), resulting in predicted (potential) loads of 15.9 and 19.5 kTonnes/year. This compared well with the 15.0 kTonnes/year predicted using SedNet and as reported in the Wilkinson et al. (2005) study, noting that this model was also uncalibrated. The trial against the EMC/DWC approach looked at temporal patterns and the role of parameter settings and the fact that dSedNet has many adjustable parameters that are not available in an EMC/DWC model. The trial against the statistically derived loads highlighted the power of dSedNet being able to incorporate spatial and temporal variation into model inputs. Simulated dSedNet loads tended to follow observed loads.

Project Impacts

As a spatially distributed model, dSedNet keeps track of spatial input data so that outputs can be traced back to their source. This is invaluable for targeting catchment remedial and intervention activities, and is not available in the current EMC/DWC model. Moving to a daily (dSedNet) from an annual (SedNet) time-step has been a significant scientific endeavour dSedNet that supports modelling of the temporal dynamics of constituents in a catchment. This supports the ability to anticipate specific events (e.g. impacts of a large flow) at different times within a year and investigate within-year variations.

Operationalising dSedNet within Australia’s national hydrological modelling platform (eWater’s Source) provides researchers, planners and catchment managers with an integrated tool to explore the impacts on the quality of receiving waters of catchment dynamics, such as gully and riparian management, urban and agricultural intensification, and environmental flows.

Research Outputs

Statistical Model for Flow and Constituent Transport in Onkaparinga Catchment

An Improved Water Quality Model for the Onkaparinga Catchment

Extending the water quality modelling capability within eWater Source – developing the dSedNet plugin

Project News

Chris Wright

Manager Water Science, DEW

Chris Wright holds significant experience in public sector senior leadership, having led policy, scientific and operational business units over the last twelve years in both State and Commonwealth government agencies. Chris has excellent experiences in leading policy and strategy formulation. He is skilled in building and maintaining networks across the public and private sectors to facilitate business delivery; leading and negotiating with others to achieve outcomes; and in bridging the science-policy gap, drawing on earlier roles in geospatial information systems (GIS) consulting. Chris’s formal qualifications include a Bachelor of Social Science, a Masters of Spatial Information Science and graduation from the AICD Company Directors course in 2019.

Dr Ilka Wallis

Senior Lecturer, Flinders University

Dr Ilka Wallis is a hydrogeologist with areas of expertise in quantitative hydrogeology and geochemistry. Ilka focuses on the development of reactive geochemical transport models which integrate fundamental processes that are normally studied in isolation (hydrogeological, mineralogical, geochemical and biochemical).

Ilka is also an Adjunct Professor, Department of Civil Engineering, University of Manitoba, Canada since 2017.

Peter Goonan

Environmental Science Branch, EPA

Peter Goonan is the Principal Aquatic Biologist in the Environmental Science Branch of the EPA. He has over 30 years’ experience monitoring the condition of aquatic ecosystems in SA and assessing the environmental effects caused by discharges, deposits and contaminants entering inland and coastal waters. He specialises in aquatic invertebrate identification and their responses to contaminants and water quality stressors. He also provides expert professional advice relating to water quality risks, regulation, policy, and strategic directions, and represents the EPA as an expert witness in court.

Dr Paul Monis

Manager, Research Stakeholders and Planning, SA Water

Dr Paul Monis is a technical expert within SA Water’s Business Services group, which provides scientific expertise to support the delivery of water and wastewater services to SA Water’s customers. He has specialist expertise in the areas of biotechnology and microbiology, with almost 20 years’ experience applying DNA-based and other technologies to address water quality challenges posed by microorganisms, especially enteric pathogens. Dr Monis also holds title of Adjunct Associate Professor at Flinders University, the University of Adelaide and UniSA.

Jennie Fluin

Principal Advisor Research Partnerships, DEW

Jennie’s role in the Department for Environment and Water (DEW) allows her to foster and strengthen opportunities for researchers to better connect with government to enable evidence-based decision making. Jennie has extensive experience working in both universities and government, allowing her to bridge the divide between the two sectors. She is focused on connecting natural resource researchers with natural resource decision makers, and facilitating fit for purpose partnerships.

Dr Tanya Doody

Principal Research Scientist, CSIRO

Dr Tanya Doody is a Principal Research Scientist working on high impact spatial eco-hydrological projects within CSIRO’s Land and Water Business Unit. Dr Doody leads the Managing Water Ecosystems Group, based in Adelaide, Albury and Canberra and has significant experience in quantifying the water requirements of vegetation and at times, their impact on water resources. This involves ecophysiological field-based research to underpin remote sensing tools to scale regionally to improve our understanding of the effect of flood regimes on the health of water-dependent ecosystems on the Murray-Darling Basin floodplains. Additional research includes investigating the ecological response of vegetation to water availability and environmental water to inform integrated basin water planning and management.

Professor Lin Crase

Dean of Programs (Accounting & Finance), UniSA

Professor Lin Crase is Professor of Economics and Dean of Programs (Accounting & Finance) at UniSA. He joined UniSA in February 2016 as Head of School of Commerce. Prior to commencing at UniSA, Lin was Professor and Director of the Centre for Water Policy and Management at La Trobe University.

Lin’s research has focused on applied economics in the context of water. He has analysed water markets and the property rights that attend them, water pricing and numerous applications of water policy. Whilst his expertise includes the Murray-Darling Basin in Australia, he has also worked on projects in south Asia, Japan and Europe. Lin has published over 100 journal articles, numerous book chapters, four books and a range of other papers and opinion pieces.

Professor Justin Brookes

Director, Water Research Centre, University of Adelaide

Justin has broad research interests in limnology and water treatment with a primary focus on coupling between hydrodynamics, biology and water quality contaminants such as cyanobacteria and pathogens. He is a founding member of the management committee of the IWA Specialist Group on Lake and Reservoir Management and member of the Steering Committee for the Global Lakes Ecological Observatory Network.

Justin has a PhD and a Bachelor of Science degree with Honours from the University of Adelaide.

Daniel Flaherty


Daniel Flaherty is the Accountant for the Goyder Institute for Water Research.

Daniel has extensive experience in higher education having worked in senior financial management roles at the University of South Australia, Flinders University and the University of Adelaide over the past 26 years. Daniel has also been a Board Director on a number of university related entities. Prior to that, Daniel has worked in a range of agencies in the Commonwealth and State Governments.

Daniel is a Fellow of CPA Australia and has a Bachelor of Economics from the University of Adelaide.

Dr Alec Rolston

Interim Director

Alec Rolston joined the Institute in 2021 as Research Program Manager of the Goyder Institute’s research projects in the Healthy Coorong, Healthy Basin program. He has extensive experience in integrated water resource management, integrated catchment management, drinking water source protection and wetland ecology, conservation and management across Europe and Australia.

Alec holds a PhD from the National University of Ireland Maynooth and has worked with An Fóram Uisce|The Water Forum and the Dundalk Institute of Technology in Ireland as well as the MANTEL Innovative Training Network across Europe.

Alec spent his early career in Adelaide working with Flinders University through the Coorong, Lower Lakes and Murray Mouth (CLLAMM) Ecology Research Cluster and within the Department for Environment and Water.

Daniel Pierce

Research and Development Officer

Daniel Pierce has managed research projects at the Goyder Institute for Water Research since November 2017 under both the second and third terms of the Institute.

Daniel brings experience in project management and knowledge transfer and application from 4 years working as a Senior Hydrogeologist in the Department for Environment and Water (DEW) in South Australia and from 13 years of private sector work in environmental management, science and engineering in Australia and the South Pacific. His work with DEW has included providing technical advice to the development and revision of Water Allocation Plans around South Australia in collaboration with researchers and policy makers, and managing a team of groundwater modellers and hydrogeologists involved in an assortment of water resource management issues.

Daniel has a Bachelor of Engineering (Hons, Environmental) and a Bachelor of Science (Geography) from the University of Western Australia.

Professor Enzo Lombi

Dean of Research, UniSA STEM

Professor Lombi’s main contributions to environmental research cover various aspects of contaminant risk assessment, biogeochemistry, ecotoxicology and waste management. Furthermore, the methodological development he has pursued in his research has provided the basis for collaborative efforts in a variety of research areas ranging from soil fertility and plant physiology to human health issues related to contaminant uptake via occupational exposure and diet. In the last few years he has been increasingly focusing on the transformation and toxicity of manufactured nanomaterials in the environment.

Dr Carmel Pollino

Research Director Land and Water, CSIRO

Dr Carmel Pollino is a Research Director for Land and Water at CSIRO. She has 20 years of experience working on water issues in Australia and throughout Asia. Carmel has degrees in science and environmental law and works across the science and policy interface. Significant areas of research in Environmental Flows, Hydrology, Ecology and Integrated River Basin Planning. Carmel is the lead and also a contributor to global working groups on water and has published widely in this domain.

Professor Bronwyn Gillanders

Head of School of Biological Sciences, The University of Adelaide

Professor Bronwyn Gillanders is interim Head of School of Biological Sciences at the University of Adelaide. Prof Gillanders completed her BSc at the University of Canterbury, MSc at the University of Otago and her PhD at the University of Sydney. She has a research background in environmental science focused predominantly on freshwater and marine ecology.

Her research interests include integrated marine management; coastal carbon opportunities; multiple use activities and cumulative impact assessment; biology, ecology and fisheries of cephalopods; stocking and provenance of fish; plastics in the marine environment including in seafood; use of fish bones (and other calcified structures) for assessing ecological and environmental change. She has trained and mentored ~70 Honours and Higher Degree Research students and shaped the future of 1000s of students through her undergraduate teaching. She is passionate about encouraging capable women to enter and remain in science careers.

Dan Jordan

Director, Water Security, Policy and Planning, Department for Environment and Water (DEW)

Dan Jordan is the Director, Water Security, Policy and Planning, Department for Environment and Water (DEW). Dan is also the Basin Officials Committee Alternate Member for South Australia.

Professor Okke Batelaan

Dean, School of the Environment, Flinders University

Professor Okke Batelaan is a graduate of the Free University of Amsterdam, Netherlands (MSc – Hydrogeology) and of the Free University Brussels, Belgium (PhD – Engineering). He worked for more than 20 years at the Free University Brussels and also led the hydrogeology group at the KU Leuven, Belgium since 2006. He was chairman of the Interuniversity Programme in Water Resources Engineering.

Since 2012 Okke Batelaan is Strategic Professor in Hydrogeology and currently Dean of the School of the Environment, Flinders University. Okke has broad experience in teaching groundwater hydrology, groundwater modelling, GIS and remote sensing for hydrological applications. He was supervisor of more than 140 MSc and 25 PhD students. He has extensive research experience and a publication record in shallow groundwater hydrology and modeling, recharge-discharge estimation and modeling, urban hydrology and distributed modelling, ecohydrology and impacts of land use and climate change on groundwater systems. He coordinated and participated in a large number of projects in Europe, Africa, South America, Asia and Australia. He is editor-in-chief of Journal of Hydrology: Regional Studies and of MDPI-Hydrology.