Measurements of fish and blue-green algae distributions were performed simultaneously in the shallow Sulejów reservoir (Poland) to check for their coexistence in space and time. An EK 60 Simrad echosounder with a horizontally beaming 200 kHz transducer was used to record the fish population, while a phycocyanin fluorescence on-line detection method was used to estimate the cyanobacterial biomass. Maps of the fish population and cyanobacteria cell distributions sampled every 20 s were produced using kriging techniques. The subsequent analysis of the distribution maps showed that concentrations of fish and algae sometimes do overlap in space and time, thus increasing the risk of fish contamination and human morbidity. More studies are required to further explore the relationship between fish and cyanobacteria.