Lake Visovac is a karstic phenomenon in the south of Croatia. It is a travertine barrage lake situated in the river Krka. Plankton community dynamics in three hydrological different parts in the lower basin of the lake was investigated. Plankton was collected monthly in a year period. All data point out that discharge, followed by temperature and total phosphorus are key factors directly influencing water properties, and through it the net phytoplankton and crustacean plankton assemblages. The portion of total variance described by the multivariate analysis is as it follows: 20.6% variance of phytoplankton and environmental data, 12.8% crustacean zooplankton and environmental data, and 29.4% of phytoplankton vs. crustacean zooplankton data.