Estuarine water quality: the CLUES estuary tool


Many of New Zealand's rivers fail to meet national guidelines for nutrient levels. NIWA has developed the Catchment Land Use & Environmental Sustainability (CLUES) estuary tool to predict the effects of land use on estuarine nutrient concentrations.

The issue

About half of New Zealand’s rivers fail to meet the national guidelines for nutrient levels (see the references tab for details). These rivers feed directly to our coasts where they impact on water quality in the receiving estuaries and coastal waters. It is therefore important to gain a comprehensive, national perspective on how land use is affecting our estuarine water quality.

Our approach

In 2009 NIWA started work on a tool that predicts the effects of land use changes on the concentration of nutrients in estuaries, through a combination of GIS and hydrodynamic models.

This new "CLUES Estuary Tool" combines three pre-existing tools

  • CLUES (Catchment Land Use Environmental System). This tool allows the prediction of water quality (i.e. nitrogen and phosphorus levels), based upon land use, in river systems draining to estuaries.
  • Coastal Explorer. This is a database of the physical properties of estuaries across New Zealand, developed over the last few years by NIWA.
  • ACER is an estuarine hydraulics modelling system. It takes nutrients, salt and water input from rivers and the ocean, and uses physical parameters from Coastal Explorer to predict concentrations of salt and nutrients in estuaries.

The combined tool enable views of water quality for all of NZ's estuaries under present and possible future land-uses.

The result

The CLUES estuary tool that NIWA developed combines CLUES, Coastal Explorer, and the ACER Estuarine hydraulics model. This enables views of estuary water quality for all of NZ's estuaries under present and potential land uses.

The model can:

  • forecast the effects of catchment development on potential nutrient levels
  • identify threatened but unmonitored estuaries
  • identify likely 'pristine' estuaries which are useful as reference conditions for setting levels of water quality indicators
  • enable hindcasting which can be used to assist with planning restoration objectives
  • assist in the design of water quality monitoring programmes to ensure wise allocation of scarce resources
  • provide a framework for enhanced understanding of the drivers of trophic status in coastal systems

The tool predicts "potential" nutrient concentrations which means it does not include trophic factors such as algal uptake.  We are comparing predictions from the tool with observations, mainly from Regional Council water quality monitoring, to examine the differences between predicted and observed concentrations and to validate the model.

The CLUES Estuary Tool addresses the NZ Coastal Policy Statement goals: Enhancement of water quality (Policy 21: identify deteriorating habitats), and Monitoring and reviewing effectiveness of NZCPS (Policy 28: Nationally consistent monitoring, reporting, perspectives).

We are currently working with Marlborough District Council to predict nutrient levels in Queen Charlotte and Pelorus Sounds using the tool.  We expect that eventually it will be transferable to councils throughout the country, and will be an important tool in setting water quality guidelines for our estuarine and coastal waters.

The animation below shows a demonstration of the CLUES estuary tool.  The animation begins with nutrient levels in the Rangaunu Estuary, in Northland, under current land use practices and goes on to predict nutrient level changes when dairy, sheep and beef farming are increased within the catchment area.

Demonstration of CLUES Estuary Tool from NIWA on Vimeo.


MfE, 2004. Water programme of action.  The effects of rural land use on water quality.  Technical working paper. July 2004 41p.

Ballantine et al., 2010. Analysis of national river water quality data for the period 1998 – 2007.  NIWA Client report: CHC2010-038. 61p.

Hume T., Snelder T., Weatherhead M., Liefting R., 2007. A controlling factor approach to estuary classification.  Journal of Ocean and Coastal Management. Volume 50, Issues 11-12, Pages 905-929.

Portilla E., Tett P., Gillibrand P.A. and Inall, M.E., 2009. Description and sensitivity analysis for the LESV model: water quality variables and the balance of organisms in a fjordic region of restricted exchange. Ecological Modelling,  doi:10.1016/j.ecolmodel.2009.05.004

Woods R. et al., 2006. The CLUES Project: Predicting the Effects of Land-Use on Water Quality – Stage II. NIWA Client Report HAM 2006-096. Prepared for Ministry of Agriculture and Forestry. 

NIWA Contacts

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Principal Scientist - Marine Ecology
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GIS Specialist
External people involved: 
Jo Hoyle
Sandy Elliot
Page last updated: 
9 August 2017
The Waitaki River mouth, just north of Oamaru, South Island. [NIWA]
A screenshot from the CLUES toolbox in ArcGIS 9.3