The article presents the results of the analysis of the surface water quality changes in selected rural catchments in the Czech Republic. Three river basins are used as examples – the Blšanka, Loučka and Olšava river basins. These river basins have been facing long-term problems with surface water quality and, as in many similar rural areas there has been lack of information on water quality changes. The areas are located in regions with different physiogeographical characteristics as well as the varying scope and intensity of socio-economic activities. Individual catchments show a range of similar aspects associated with the distribution of pollution load and trends of the surface water quality. However, at the same time, many differences in the dynamics of trends of changes in water quality development exist. In spite of the fact that the crucial problems concerning the surface water pollution are similar, they differ in the characteristics of time changes in water quality as well as in the spatial distribution of load within the water basin. Due to the low average discharges of all recipients, both local municipal and industrial point sources of pollution play significant roles there however they are scarce. Considering the majority of basic indicators, long-term negative trends concerning the water quality development are observed in all assessed river basins. This trend, typical for many rural areas is opposite to the water quality development at the main river courses. Moreover, because of continuing intensive load from the non-point sources no significant improvement in water quality can be expected in the near future. The adoption of effective measures is currently hindered in part by the deferral of the application of the European legislation in the area of the construction of waste water treatment plants at middle-sized and small-sized settlements.