The aim of the study was assessment of changes in nutrient concentrations in Estonian rivers as a response to improved wastewater treatment and substantial reductions in the use of fertilisers and number of livestock during the past 15–20 years. A Mann–Kendall test and flow adjusted technique to assess recent trends have been used. Statistical analysis covered time series of 53 sampling sites on 40 rivers and streams in different hydro-geographical regions and varying human pressures. The results indicate a statistically significant downward trend in nitrogen concentration in 18 sampling stations during the studied period; only very few showed an upward trend. These decreases in total nitrogen (TN) relate mainly to (i) substantial reductions in the use of fertilisers, (ii) decreased area of agricultural land, (iii) decreased point source load and (iv) increased self-purification capacity of soil-water systems. The concentration of phosphorus decreased only in 13 locations, despite of efforts to improve the efficiency of wastewater treatment. Moreover, in seven locations the concentration of phosphorus was increasing. This increase in total phosphorus (TP) probably relates to the low treatment efficiency of small wastewater treatment facilities as well as to the raised ground water table due to insufficient maintenance of drainage systems that favour transport of soil P to water bodies. Accordingly, the ratio of nitrogen and phosphorus had both decreasing and increasing trends.