This data file contains processed data derived from the Environment Agency's Ecology and Fish Explorer Macroinvertebrate database. The recorded data is the abundance of freshwater macroinvertebrates taken by the Environment Agency (EA). The data were collected from sites throughout England, between 2002-2019, from March to May, and September to November. Samples were collected using three-minute kick-samples, whereby a net is used to catch invertebrates and debris flowing downstream of an area in a river which is disturbed by a recorder for three minutes. Data before 2002 were excluded as abundance of macroinvertebrates was not recorded widely before this year. The data were originally collected for the purpose of understanding water quality by the Environment Agency. The original EA data contains raw counts of mixed-taxonomic groupings of invertebrates and some diatoms and other taxa, from rivers in England with multiple sampling methodologies. Here, the derived data has been processed in such a way to combine counts at a single taxonomic level (family) containing only taxonomic groups of interest for the research, and the data are limited to one sampling method. Full details about this dataset can be found at https://doi.org/10.5285/f6b9b2b3-1ad0-4ac1-a19b-bb340427fbf1