The diversity of natural conditions as well as the industrial and agricultural character of the landscape are responsible for changes influencing the share of point and nonpoint sources of pollution in the Morava River basin. Nonpoint sources of pollution were specified on the basis of data on agriculture, forestry, erosion, suspended solids, water quality parameters, mass flow of nutrients and atmospheric deposition. The relationship between concentrations of nitrates and application rates of mineral nitrogen fertilizers in the lower part of the Morava River basin was significant. In the longitudinal profile of the Morava River concentrations of mineral nitrogen and total phosphorus were specified and mass flow calculated by characteristic discharge. Changes of political system in 1989 in the Czech Republic initiated dynamic development of the state agricultural policy with consequences for the intensity of nonpoint pollution. Mainly in the field of plant and animal production some influences were evidently reduced. Consumption of industrial fertilizers was minimized to 1/3 of the former level and livestock population was also significantly decreased. Although privatization in agriculture is practicaly finished, there are not many positive changes in the field of large-area land use and structure of plots. The process of soil erosion still causes damages of land and pollution of surface waters.