This data release incorporates high-resolution geospatial and biological data and accompanies a peer-reviewed manuscript "Specialized meltwater biodiversity persists despite widespread deglaciation". In this study, we tested the prediction that glacier retreat reduces biodiversity in mountain ecosystems through the loss of uniquely adapted meltwater stream species in Glacier National Park, USA. This dataset, "Glacier National Park alpine aquatic invertebrates, 2011-2013", includes location and landscape data, as well as quantitative aquatic macroinvertebrate community data for 129 collection sites within Glacier National Park. Additionally, this dataset includes watershed drainage area, area of ice and perennial snow cover for all sites, calculated using two geospatial datasets. The dataset "Minimum snow and ice coverage for GNP, 2003-2015" is a GIS shapefile of the minimum extent of glaciers and multi-year snow features digitized from satellite imagery. The dataset "Glacier National Park alpine stream sampling watersheds, 2011-2013" is a GIS shapefile of the drainage areas of each of the 129 alpine and glacial aquatic macroinvertebrate collection sites included in the analysis. The proportion of contemporary ice and snow coverage for each collecting site was calculated from the watershed drainage area, then compared to glacier coverage from the peak of the Little Ice Age (ca. 1850).