Zooplankton abundance and diversity of Salado and Negro rivers were compared in relation to the water level fluctuations. The zooplankton pumper samples were collected between March, 1993 and October, 1994. Mean zooplankton density at Salado river was very higher in upstreem. Zooplankton density in the Negro and Salado rivers were variable in the high water phase. Changes in the density appeared to be related to the hydrologic phases, seasonal cycle and conductivity variation. The zooplankton abundance was positively correlated with the abiotic and biotic factors (temperature, transparency and fitoplankton). The dominant group in the two studied rivers were the rotifers. The dominant species in the high water phase were limnoplanktonic and scarce ticoplanktonic organisms, in the low water phase the present organisms were euryhalin. The highest diversity was taken in the Negro river with major floodplain. The Jaccard Index (1908 ) showed no similarity zooplankton between Salado and Negro rivers.