Freshwater physical habitat: Data to 2024

Methodology: Habitat quality score (HQS) The Rapid Habitat Assessment (RHA) is a field survey protocol that provides a semi-quantitative standardised assessment of the physical habitat condition of New Zealand’s wadeable rivers and streams at the reach level (Clapcott, 2015). RHA involves qualitative scoring of ten habitat parameters at each assessed site: deposited sediment, invertebrate habitat diversity, invertebrate habitat abundance, fish cover abundance, fish cover diversity, hydraulic heterogeneity, bank erosion, bank vegetation, riparian width, and riparian shade. These scores are added together to produce a habitat quality score (HQS) that indicates the overall state of stream habitat at the monitored site. HQS scales from 10 to 100, with low scores indicating lower habitat quality and high scores indicating higher habitat quality. Eveleens et al., 2025 describes the ten habitat parameters: Deposited sediment: visual estimate of the extent of fine sediment (sand and silt < 2 mm in size) covering the streambed. Excessive fine sediment can smother habitat, reduce oxygen availability and degrade conditions for invertebrates and fish; therefore, areas with less fine sediment cover are given a higher score. Invertebrate habitat diversity: the range of available microhabitats for aquatic invertebrates (e.g. cobbles, gravels, macrophytes, woody debris). Greater diversity supports higher species richness; therefore, areas with more microhabitats – including the presence of interstitial spaces – are given a higher score. Invertebrate habitat abundance: quantity and extent of instream habitats favourable for sensitive aquatic invertebrates such as stonefly, mayfly and caddisfly; for example, flowing water over gravel-cobbles clear of filamentous algae / macrophytes. Higher abundance increases opportunities for colonisation and productivity; therefore, a greater proportion of favourable substrate is given a higher score. Fish cover density: the number of different substrate types with the potential to provide instream cover for fish; substrate types include woody debris, root mats, undercut banks, overhanging / encroaching vegetation, macrophytes, boulders and cobbles. A diverse array of cover supports different life stages and species with varying habitat preferences; therefore, areas with more substrate types and the presence of substrates providing spatial complexity are given a higher score. Fish cover abundance: the amount of instream cover available for fish. Adequate cover is critical for shelter, feeding and predator avoidance; therefore, areas with more cover are given a higher score. Hydraulic heterogeneity: variation in flow types (e.g. riffles, runs, pools, backwaters) within a reach. Greater heterogeneity provides habitat mosaics that sustain ecological complexity; therefore, areas with more hydraulic components and the presence of deep pools are given a higher score. Bank erosion: extent and severity of streambank instability or active erosion due to scouring at the waterline, slumping of the bank or stock pugging. High erosion can contribute sediment loads and indicate loss of riparian or geomorphic integrity; therefore, areas with less erosion are given a higher score. Bank vegetation: condition and type of vegetation stabilising streambanks. Healthy, well-vegetated banks reduce erosion, filter run-off and provide habitat. More established vegetation and a greater diversity of species scores higher. Riparian width: width of vegetated riparian buffer alongside the stream constrained by vegetation, fences or other structures. Wider buffers enhance habitat quality, regulate microclimate and intercept pollutants; therefore, areas with a wider riparian buffer are given a higher score. Riparian shade: degree of shading of the stream channel throughout the day provided by riparian vegetation, banks or other structures. Adequate shading helps regulate water temperature, control nuisance plant growth and maintain habitat quality; therefore, areas with more shade are given a higher score. This indicator uses the interpretation of HQS and habitat condition provided in Clapcott et al., 2020. That is, habitat condition is: ‘Excellent’ when HQS is above 75 ‘Good’ when HQS is above 50 but less than or equal to 75 ‘Fair’ when HQS is above 25 but less than or equal to 50 ‘Poor’ when HQS is less than or equal to 25. Current state We report on the current state of Aotearoa New Zealand’s freshwater physical habitat using the median HQS, calculated from data recorded at monitored river sites between 2020 and 2024. Sites required at least one observation per year for at least three years during the period. This minimum data requirement reduces statistical bias and allows consistent comparisons between sites by ensuring the same period was considered. A total of 814 sites from across 12 regions met this minimum data requirement. Table 1: Number of sites in current state analysis between 2020 and 2024 by council. Council Number of sites in current state analysis Environment Canterbury 164 Environment Southland 101 Gisborne District Council 71 Greater Wellington Regional Council 50 Hawke’s Bay Regional Council 72 Horizons Regional Council 85 Nelson City Council 7 Northland Regional Council 32 Otago Regional Council 46 Taranaki Regional Council 68 Waikato Regional Council 87 West Coast Regional Council 31 Change in habitat condition We report on changes in Aotearoa New Zealand’s freshwater physical habitat using the median HQS, calculated from data recorded at sites for two time periods: 2015–2019 and 2020–2024. Sites required at least one observation per year for at least three years during each period. This minimum data requirement reduces statistical bias and allows consistent comparisons between sites by ensuring the same periods were considered. A total of 432 sites from across 8 regions met this minimum data requirement. Table 2: Number of sites in change analysis for two periods, 2015–2019 and 2020–2024, by council. Council Number of sites in change analysis Environment Southland 95 Gisborne District Council 66 Greater Wellington Regional Council 39 Hawke’s Bay Regional Council 46 Northland Regional Council 28 Otago Regional Council 14 Taranaki Regional Council 58 Waikato Regional Council 86 Human modified land cover Catchment land use reflects the extent of human modified land cover and is an important pressure on river habitats. Although individual habitat parameters contribute differently to overall habitat quality scores, comparing these scores with the percentage of human‑modified land cover helps us understand the relationship between land use and habitat condition. We report on the correlation between human modified land cover in a catchment and freshwater physical habitat at a site by calculating what proportion of land in the upstream catchment has been developed or otherwise transformed to support human uses for each site’s river segment. To measure this, we used the New Zealand Land Cover Database version 6.0 (LCDB v6.0). We included the following detailed land cover classes as human modification: Built-up area (settlement) Urban parkland/open space Transport infrastructure Surface mine or dump High producing exotic grassland Short-rotation cropland Orchard, vineyard or other perennial crop Exotic forest Forest - harvested Of the 814 sites that met the minimum data requirements to calculate median HQS between 2020 and 2024, 792 sites from across 11 regions were able to be linked to a river segment in the River Environment Classification (REC) river network, which subsequently allowed matching to the LCDB v6.0. Table 3: Number of sites in land cover analysis between 2020 and 2024, by council. Council Number of sites in land cover analysis Environment Canterbury 161 Environment Southland 101 Gisborne District Council 71 Greater Wellington Regional Council 50 Hawke’s Bay Regional Council 72 Horizons Regional Council 85 Northland Regional Council 27 Otago Regional Council 40 Taranaki Regional Council 68 Waikato Regional Council 86 West Coast Regional Council 31 Data source Cawthron Institute collated RHA data and associated metadata from 15 regional councils and unitary authorities for the period 2013 to 2024. Auckland Council advised that they do not collect habitat data using the RHA protocol, so no data from Auckland sites is included in this indicator (Eveleens et al., 2025). Cawthron Institute compiled data for 1,619 unique sites across Aotearoa New Zealand. In addition to the Auckland Region, there are spatial gaps in the Tasman Region and the lower West Coast / Fiordland (Eveleens et al., 2025). Sites included both long-term monitoring sites within state of the environment programmes and sites monitored as part of short-term targeted investigations. The length of sample records ranged from one to nine years per site. Limitations While some councils have previously collected (e.g. Greater Wellington, Horizons and Otago Regional Councils) or continue to collect (e.g. Bay of Plenty Regional Council) habitat data using a draft version of the RHA (Clapcott 2013), the scope of this project was restricted to data collected using the finalised protocol. The final RHA method was published in January 2015, meaning there is no nationally standardised dataset available prior to this date. From 2015 onward, however, the consistent application of the RHA across most regions provides a robust basis for national reporting and strengthens the potential for reliable state and trend analyses of stream habitat condition (Eveleens et al., 2025). RHA is applied mainly at wadeable state of the environment monitoring sites. National estimates of river habitat condition derived from collated RHA data are likely to under-represent very small and very large native-forest rivers and over-represent degraded lowland or pastoral systems (Eveleens et al., 2025). Freshwater physical habitat trends were not computed because site-level data were too variable to detect “meaningful” trends in the relatively short time period between 2015 and 2024. Eveleens et al., (2025) defined a meaningful trend as an increase or decrease in HQS of 25, to represent an average change of at least one point for each parameter beyond the 15 percent inter-user variability identified during the development of the RHA protocol (Clapcott, 2015). Power analyses performed by Eveleens et al., (2025) determined the minimum number of years needed to detect trends under different assumptions. Catchment land cover is compared with HQS because quality land cover data is readily accessible, and land cover can affect several important aspects of river physical habitat. However, land cover does not influence all measured parameters that determine HQS and influences different parameters to varying degrees. The reported river habitat condition may therefore be affected by other pressures that are not captured in this analysis. References Clapcott J. 2013. Rapid Habitat Assessment workshop. Nelson: Cawthron Institute. Cawthron Report No. 2445. Prepared for Hawke’s Bay Regional Council. Clapcott, J. (2015). National rapid habitat assessment protocol development for streams and rivers. Prepared for Northland Regional Council. Cawthron Report No. 2649. Clapcott J, Casanovas P, Doehring K. 2020. Indicators of freshwater quality based on deposited sediment and Rapid Habitat Assessment. Cawthron Report No. 3402. Prepared for Ministry for the Environment. Eveleens, R., Lee, F., Kelly, L., Clapcott, J. (2025). Update to freshwater physical habitat statistics for environmental reporting. Prepared for Ministry for the Environment. Cawthron Report No. 4196. Harding, J., Clapcott, J., Quinn, J., Hayes, J., Joy, M.K., Storey, R.G., Greig, H.S., Hay, J., James, T., Beech, M.A., Ozane, R., Meredith, A.S., Boothroyd, I.K.G. (2009). Stream Habitat Assessment Protocols for wadeable rivers and streams of New Zealand. School of Biological Sciences, Christchurch. Maddock, I. (1999). The importance of physical habitat assessment for evaluating river health. Freshwater Biology (1999) 41, 373–391. en-NZ