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CLUES – Catchment Land Use for Environmental Sustainability model

NIWA’s Catchment Land Use for Environmental Sustainability (CLUES) model is a GIS-based system that predicts the effects of land-use change and farm practice scenarios on water quality and a range of socio-economic indicators at the catchment scale.  CLUES allows users to create land use change and land management scenarios and view results in map or tabular displays.  It was developed as a decision support tool for catchment managers, land-use planners and regulators and is available publicly for non-commercial use. 

CLUES was developed by NIWA for the Ministry of Agriculture and Forestry (now part of the Ministry for Primary Industries) and the Ministry for the Environment and contains aspects of three existing water quality models (SPARROW, OVERSEER and SPASMO) as well as a socio-economic model. Various agencies contributed to the development of CLUES   including AgResearch, Landcare Research, Plant & Food Research, Aqualinc Research and Harris Consulting.   

CLUES is provided as a front-end interface for ArcMap and comes with a geospatial database that includes land use for the base year 2018 and stream data from the River Environments Classification, REC. The GIS platform allows geo-visualisation of both the model input data and model outputs.  Users can also add their own spatial data for display and to create scenarios.  

For each river reach in the REC stream network, CLUES predicts the annual average loads and yields of nutrients (total nitrogen and total phosphorus), total suspended solids and E. coli. Estimates of nutrient concentrations are also calculated.  Social economic indicators include farm revenue and employment, fuel and energy use and greenhouse gas emissions.  


Estuaries support sensitive ecosystems and are the receiving environments for stream and river catchments. The CLUES Estuary tool has been integrated into the CLUES model system to help manage these ecosystems. This tool predicts potential nutrient (nitrates and total phosphorus) concentrations in estuarine environments and can be run with the same scenarios as CLUES. For more information, visit the CLUES Estuaries homepage.   

Model requirements and downloads 

CLUES is installed as an addin to ArcMap; you will need access to ArcMap 10.6 or 10.8 to run CLUES.  We are currently working on transferring CLUES to ArcPro with a new release planned for 2023. 

CLUES is available for download free of charge for non-commercial use, downloading and using CLUES implies that you have read and accept the user licencing agreement.  CLUES software, documentation and data files can be downloaded from the links below.  

Download type 


N.B. some of these files are very large

Addin_Arcmap10.6 and 10.8 

Zip folder containing the CLUE model software as an ArcMap plugin 

Regional geodatabases 

Zip folders holding the shapefiles of region specific data for CLUES.  

One zip file link for each of the 10 regions:

Canterbury  [523MB zip file]

North Island east [498MB zip file]

north Auckland [168MB zip file]

Otago  [262MB zip file]

South [ 337MB zip file]

Taranaki  [357MB zip file]

Tasman  [164MB zip file]

West Coast  [222MB zip file]

Waikato  [229MB zip file]

Wellington [106MB zip file]

CLUES scenario builder 

Python tool for automatically populating CLUES land management scenarios.  Zip folder contains the tool and spatial data by region. 

CLUES scenario builder [118MB zip file containing the tool and data files] 


CLUES manual, licensing agreement and development reports. 

CLUES documentation [18MB zip file containing document PDFs] 

Farm Practice Template 

Spreadsheet for creating land management text files tor the manual development of land management scenarios         

Farm Practice Template [Spreadsheet]


Publications list:

Plew, D., Zeldis, J., Shankar, U., & Elliot, S. (2015, 15 - 18 September 2015). CLUES Estuary – a tool for predicting estuary water quality Australasian Coasts & Ports Conference, Auckland, New Zealand.

Semadeni-Davies, A., Elliot, S., & Shankar, U. (2016) CLUES - Catchment Land Use for Environmental Sustainability User Manual Fifth Edition: CLUES 10.3, NIWA internal report: AKL2016-017. Link below

Semadeni-Davies, A., Elliott, S., & Shankar, U. (2014). How CLUES can help in managing catchment nutrient limits. In: Nutrient management for the farm, catchment and community. In L. D. Currie & C. L. Christensen (Eds.), Occasional Report No. 27. Fertilizer and Lime Research Centre.

Semadeni-Davies, A., Jones-Todd, C., Srinivasan, M. S., Muirhead, R., Elliott, A., Shankar, U., & Tanner, C. (2020). CLUES model calibration and its implications for estimating contaminant attenuation. Agricultural Water Management, 105853.    

Semadeni-Davies, A. F., Jones-Todd, C. M., Srinivasan, M. S., Muirhead, R. W., Elliott, A. H., Shankar, U., & Tanner, C. C. (2019). CLUES model calibration: residual analysis to investigate potential sources of model error. New Zealand Journal of Agricultural Research, 1-24.               

·         Showcase NIWAs capabilities in the area of mitigation systems with videos on constructed wetlands and riparian buffers.

  • Update the mitigations systems programme webpages on the NIWA website to reflect up-to-date priorities and projects.


CLUES Estuaries run with default land use for Raglan Harbour
CLUES model outputs are available in map and tabular form.  CLUES run showing increased nutrient loads due to conversion of forest to dairy.