Abstract 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 improved regulation of fertiliser usage and wastewater treatment are reflected as declining riverine nutrient concentrations, with the largest relative improvements occurring in catchments with initially high proportions of point source loading. We analysed nutrient dynamics in 16 rivers differing by catchment land use, population and livestock densities. Data on fertiliser use and wastewater treatment originated from the Statistics Estonia database, and riverine nutrient concentrations from the State Environmental Monitoring Database. We clustered the rivers by their catchment properties and analysed trends in their nutrient status. Point source nutrient loading reductions explained most of the decline in riverine nutrient concentrations, whereas 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.