The research results of water supply reservoirs and their tributaries in the Morava River basin showed the important role of the biological and microbiological investigations by monitoring the influence of diffuse pollution on the reservoir's water quality. Our report brings the critical evaluation of the possibility to use some microbiological and biological methods by monitoring of diffuse pollution, it also includes some practical results received from monitoring the streams and reservoirs within the Morava River basin (in the frame of research projects of the T. G. Masaryk Water Research Institute, branch office Brno).