Diffuse (nonpoint) pollution from the river basin is responsible for a substantial part of Czech reservoirs' deterioration caused by eutrophication and water pollution. The research results of two model drinking water supply reservoirs (different area and depth) in the Morava river basin showed that the main nutrient sources in the period 1960-1991 were: agricultural land use (overland and subsurface transport of nutrients, effects of drainage and erosion), point sources (urban activities, agricultural farms) and atmospheric depositions of N and P compounds. The accelerated eutrophication was manifested by the increasing development of phytoplankton. The main problems entail occurrence of toxic species of Cyanophyta/Cyanobacteria (blue-green algae) Aphanizomenon flos-aquae, Microcystis aeruginosa and some other species (e.g. Pseudanabaena limnetica). In the small and shallow drinking water reservoir of Ludkovice the living algae penetrated drinking water. In the deep reservoir of Vír the situation was more favourable. The increase of nutrient input (N,P) during the period 1969-1992 was highly significant Various measures have been proposed to slow the reservoir eutrophication (sustainable use of land, best management practices - soil retention, buffer strips, constructed wetlands etc.).