Many waterbodies undergo nutrient decline, called oligotrophication, globally, but a comprehensive dataset to understand ecosystem responses is lacking. The OLIGOTREND database comprises multi-decadal chlorophyll a and nutrient time series from rivers, lakes, and estuaries with 4.3 million observations from 1894 unique measurement locations. The database provides empirical evidence for oligotrophication responses with a spatial and temporal coverage that exceeds previous efforts.