The composition and distribution of the phytoseston communities and heterotrophic bacteria from the Wełna and Nielba rivers before and behind the cross-rivers were analyzed from June to September 2007. In both rivers the highest concentration of algae biomass were recorded in July and September, which was connected with concentrating the periphytic and benthic species in phytoseston, during which the influence of the increasing water level were transported into the lower part of rivers. Algae such as Gomphonema parvulum, Tychonema granulatum, Cryptomonas ovata, Aulacoseira granulata, Cocconeis placentula, Monoraphidium contortum, Planctolyngbya limnetica, Cyclotella radiosa, and Fragilaria ulna var. angustissima were the most common species for all examined sites. Furthermore, the results indicate that at sites located along the Wełna and Nielba rivers a trend of diatom increase in the biomass was observed behind the crossing. In this study we found that diatoms and green algae dominated in the Nielba river, while cyanobacteria domination was typical for the Wełna mainly before the crossing rivers. The analysis of the number of psychrophilic and mesophilic bacteria indicated the greater number of bacteria in the Wełna river compared to the Nielba. We think that the process of mixing waters of two rivers are responsible for the reduction in bacterial cell numbers in the Wełna water.