Catchment Land Use for Environmental Sustainability (CLUES)


CLUES is a catchment-based model developed to address “what if” scenarios under different land use at large scales. CLUES predicts the impacts of land use changes on river quality and socio-economic indicators, e.g. GDP, or employment. It also identifies sensitive and at risk catchments.


CLUES is a modelling system for assessing the effects of land use change on water quality and socio-economic factors at a minimum scale of sub-catchments (~10 km2 and above). CLUES was developed for the Ministry of Agriculture and Forestry (MAF) in association with the Ministry for the Environment (MfE) by NIWA, in collaboration with Lincoln Ventures, Harris Consulting, AgResearch, HortResearch, Crop and Food Research, and Landcare Research.

CLUES couples a number of existing models within a GIS-platform and is provided to users as a front-end interface for ArcGIS which queries a geo-spatial database. The CLUES interface has tools which allow users to develop land use change and farm practice scenarios. The latter refer to percentate adjustments to stocking rates and contaminant yields from stock. CLUES models nitrogen and phosphorus loads in streams in specific locations under different land-use scenarios. Links to socio-economic models mean that the effects of a large-scale change in land-use, say from grazing livestock to viticulture, on local communities can also be predicted.

The CLUES project includes creating national maps of land use, soils, and pollution risk, plus extensive databases predicting nitrogen leaching for many combinations of crop, fertiliser, climate, and soils. Land-use types which can be analysed include arable, horticulture, forestry, and several sheep, beef, dairy, and deer farming variations.

The initial impetus for CLUES development came from MAF, who wanted 'what if'' scenarios to be modelled at large scales. A number of existing modelling and mapping procedures, developed by various research organisations, have been amalgamated to produce CLUES.

CLUES has also been linked to an estuarine model

Latest Version CLUES 10 for ArcGIS 10
State of Development Released and updated

Development Contact

Sandy Elliott
+64 7 856 7026
National Institute of Water and Atmospheric Research
Gate 10 Silverdale Road
Hillcrest, Hamilton 3216
PO Box 11115, Hamilton,
New Zealand

Main Developers

  • Landcare Research
  • National Institute of Water and Atmospheric Research (NIWA)
  • AgResearch
  • Plant and Food Research
  • Harris Consulting


Outcome Areas Economic, Environmental
Management Domains Land, Freshwater
Subdomains Contaminant Losses
Intended End Users
  • Regional Council Scientist
  • Researcher
  • Regional Councils
Spatial Resolutions 10-100m
Spatial Extents Regional
Spatial Dimensions 2D
Temporal Resolutions Years
Temporal Extents Years
Steady State or Dynamic Steady State
Level of Integration Economic, Environmental

Input & Output Data

Key Input Data Macro-economic data, Land Use, Land Cover, Rainfall, Runoff, Drainage
Input Data Formats CSV, GIS compatible files
Key Output Data Runoff Water quality
Output Data Formats CSV, Image File(s), GIS Compatible Files


Open/Closed Source Closed Source
Licence Type Licence appended to manual.
Licence Cost
(Non Commercial)
Licence Cost
Price negotiable
Licence Purchase Contact
Sandy Elliott

User Information

Operating Systems MS Windows
Software Needed ArcGIS
User Interface Graphical desktop
Ease of Use Moderate
Use in Policy Process Plan (Policy Formulation), Review (Issue Identification)

CLUES Manual 5th Edition - June 2016

Download background reports, software and manual from NIWA ftp site

Support Ongoing maintenance and support - contact
Users Forum Regular updates available upon registration to user group - contact

Technical Considerations

Methods included for calibration and validation See manual
Analytical Techniques GIS
Model Structure


See manual for further detail.

Keywords land use, water quality, socio-economic, catchment
Linkages to other Models

CLUES Estuary - Plew, D., Zeldis, J., Shankar, U., Elliot,S. (2015) CLUES Estuary – a tool for predicting estuary water quality. Australasian Coasts & Ports Conference, Auckland, New Zealand.

Key References

Semadeni-Davies, A.; Elliott, S. and Shankar, U. (2014): How CLUES can help in Managing Catchment Nutrient Limits. NIWA Paper

Semadeni-Davies, A., Shankar, U. and Elliott, S. (2012): CLUES 10 Installation and Interface: Addendum to the CLUES 3.1 User Manual. Prepared for the Ministry of Agriculture and Forestry. NIWA Client Report: AKL2012-007.

Semadeni-Davies, A.; Elliott, S. and Shankar, U. (2011): The CLUES Project: Tutorial manual for CLUES 3.0. Commissioned by Ministry of Agriculture and Forestry, NIWA Client Report: HAM2011-003

Elliott, A.H, et, al,.(2016): A national-scale GIS-based system for modelling impacts of land use on water quality. Environmental Modelling & Software, Volume 86,Pages 131-144.

Woods, R.; Elliott, S.; Shankar, U.; Bidwell, V.; Harris, S.; Wheeler, D.; Clothier, B.; Green, S.; Hewitt, A.; Gibb, R. & Parfitt, R. (2006). The CLUES Project: Predicting the Effects of Land use on Water Quality – Stage II. Prepared for Ministry of Agriculture and Forestry by NIWA, Client Report: CHC2006–096

Monaghan, R.M.; Semadeni-Davies, A.; Muirhead, R.W. Elliott S. and Shankar U. (2010) Land use and land management risks to water quality in Southland. AgResearch Client Report, prepared for Environment Southland.

McBride, G.B.; Rys, G.; Elliott, S.; Shankar, U.; Semadeni-Davies, A. (2008). "CLUES: Do we have any idea about the nutrient impacts of land use change at the catchment level?" Fertiliser & Lime Research Centre, Massey University, 21st Annual Workshop: Carbon and nutrient management in agriculture: Addressing the hard questions. 13–15 February.

Associated Case Studies

CLUES - Mataura River, Southland

Environment Southland contracted NIWA to simulate the effects of land use change and farm mitigation practices on water quality (loads and concentrations of total nitrogen (TN) and total phosphorous (TP) for the Mataura River catchment (5350 km2) using the CLUES 3.0 model.


CLUES - Northland Sediment: E Coli Study

The CLUES model was used as a part of the Northland Sediment Study (NSS) which had the aim of assessing the potential economic costs of achieving sediment and microbial water quality objectives in the Whangarei Harbour catchment area.


Other Key Case Studies

Waitaki River Water Quality (Canterbury): Palliser et al 2015 Waitaki Water Quality Catchment Modelling Report prepared by NIWA for  Environment Canterbury

Northland Sediment Study: E. coli modelling -

Modelling the potential impact of New Zealand’s freshwater reforms on land-based Greenhouse Gas emissions -