A positive relationship between occupancy and average local abundance of species is found in a variety of taxa, yet the mechanisms driving this association between abundance and occupancy are still enigmatic. Here we show that freshwater fishes exhibit a positive abundance-occupancy relationship across 125 Swedish lakes. For a subset of 9 species from 11 lakes, we estimated species-specific diet breadth from stable isotopes, within-lake habitat breadth from catch data for littoral and pelagic nets, adaptive potential from genetic diversity, abiotic niche position, and dispersal capacity. Average local abundance was mainly positively associated with both within-lake habitat and diet breadth, that is, species with larger intraspecific variation in niche space had higher abundances. No measure was a good predictor of occupancy, indicating that occupancy may be more directly related to abundance or abiotic conditions than to niche breadth per se. This study suggests a link between intraspecific niche variation and a positive abundance-occupancy relationship and implies that management of freshwater fish communities, whether to conserve threatened or control invasive species, should initially be aimed at niche processes.