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The number of New Zealand's freshwater fish listed as threatened has increased since 1992 when the first New Zealand threat classification system list was compiled. In this study, temporal and land cover-related trends were analysed for data on freshwater fish distribution, comprising more than 20 000 records for the 47 years from January 1970 to January 2017 from the New Zealand Freshwater Fish Database. The analysis included individual species abundance and distribution trends, as well as an index of fish community integrity, namely the Index of Biotic Integrity (IBI). Of the 25 fish species that met the requirements for analysis to determine changes in the proportion of sites they occupied over time, 76% had negative trends (indicating declining occurrence). Of the 20 native species analysed for the proportion of sites occupied over time, 75% had negative trends; 65% of these were significant declines and more species were in decline at pasture sites than natural cover sites. The average IBI score also declined over the time period and, when analysed separately, the major land cover types revealed that the IBI declined at pasture catchment sites but not at sites with natural vegetation catchments.