Eutrophication caused by excess nutrient loads is the main problem for Estonian surface waters. The assessment of the type of human activity on the catchment area that may cause an impact on the status of a water body is needed for successful implementation of the Water Framework Directive. The lack of necessary information often makes it difficult to perform this task. The simple export coefficients approach has been used in this investigation for evaluation of the impact of different sources of nutrients on the water quality in Estonian rivers. Attention has mainly been concentrated on the diffuse pollution sources (natural and anthropogenic). Nonlinear regression was used for the estimation of the export coefficients and retention of nutrients. Results revealed that the export coefficients vary within a wide range of limits even in such a small country as Estonia. Soil type, topography, climatic conditions and water flow are the main natural factors influencing export coefficients. It was demonstrated that the use of export coefficients estimated for other regions may lead to wrong conclusions about the impact of different diffuse sources on the water body status.