We analysed long-term (1992–2020) changes in fertiliser use, wastewater treatment, and river water nutrient status in Estonia (N-E Europe) in the context of changing socio-economic situations and legislation. We hypothesised that more precise regulation of fertiliser usage and improved wastewater treatment are reflected as declining riverine nutrient concentrations, and that the largest relative improvements occurred in catchments with initially high proportions of point source loading. We used data on population and livestock densities, fertiliser use, and wastewater treatment from the Statistics Estonia database and riverine nutrient concentrations from the environmental monitoring database. We clustered the rivers by their catchment properties and analysed trends and step changes in their nutrient status. Point source nutrient loading reductions explained most of the observed decline in riverine nitrogen and phosphorus concentrations, whereas the application of mineral fertilisers has increased, hindering efforts to reach water quality and nutrient load targets set by the EU Water Framework Directive and the Baltic Sea Action Plan. Highest nitrogen concentrations and strongest increasing trends were found in rivers within the nitrate vulnerable zone, indicating violation of the EU Nitrates Directive. To comply with these directives, resource managers must address non-point source nutrient loading from river watersheds.
Drop in point source loading explained the decline in riverine nitrogen (N) and phosphorus (P) since 1994.
Fertiliser and wastewater management measures fail short to meet the water quality and nutrient load targets set by the EU Water Framework Directive.
Highest N concentrations and strongest increasing trends were found in rivers within the nitrate vulnerable zone violating the EU Nitrates Directive.