The Bydgoszcz Channel is an important artificial channel connecting two of the largest rivers and their catchments in Poland and in central Europe, the Vistula and Odra. It is also the main vector connecting the Noteć River from the East and near the mouth to Brda river from the West. Except for hydrography the Bydgoszcz Channel is also an interesting artificial river from the ecological point of view. In the present study we identified and compared the zooplankton community along with physicochemical and biological properties. Water samples were collected on Bydgoszcz Channel and Notecki Channel monthly during the spring (April 2019 to June 2019). We investigated how the flow of the channel and its tributary affected the various physicochemical and biological conditions (including water temperature, water transparency, dissolved oxygen, saturation, conductivity, pH, nitrate, phosphate and Chl-a concentration). These analysed parameters in turn affected the seasonal variations of zooplankton diversity (T) and density (N). The zooplankton community was dominated by rotifers and crustaceans. During May we recorded the highest rotifer density (N Rot) 2090 ind/L in Bydgoszcz Channel with an average 1256 ind/L and highest rotifer diversity (T Rot) of 20 species. The most dominant were Keratella cochlearis, Keratella quadrata, Polyarthra dolichoptera. The highest crustacean density (N Crust) was recorded during June on Bydgoszcz Channel 1420 ind/L with an average of 564.5 ind/L and diversity (T Crust) of 8 species recorded from Notecki Channel. The most dominant species among crustaceans was the cladoceran Bosmina longirostris. We assume that the crustacean diversity, density and biomass increased due to increasing temperature. On the contrary, the rotifers species decreased. It follows that adult copepods and their larval stages copepodites could eat small rotifers causing a decline in the number of rotifers. It is also possible that the decline in rotifer numbers could have been caused by competition for food with the Cladocera.