The distribution of zooplankton communities from the source to the mouth of a lowland water course, the Scheldt, was used to test some concepts on the longitudinal distribution of organisms along both estuarine (Remane’s diversity concept) and riverine reaches (River Continuum Concept (RCC), Riverine Ecosystem Synthesis (RES)). Substantial zooplankton densities were found in both April and June samples all along the water course, and not only in the lower reaches as suggested by the RCC. Based on the zooplankton communities, and using hierarchical classifications and Generalized Linear Model, several successive zones influenced by different physical and chemical variables and trophic conditions could be distinguished along the Scheldt, in agreement with the RES model: the non-tidal riverine, the tidal freshwater, the tidal salinity gradient, and the marine zones. Over the entire freshwater reach, rotifers were numerically dominant during both samplings; crustaceans became more abundant in June than in April, specifically in the downstream reaches. Highest total zooplankton abundance and diversity were found in the tidal freshwater reach, lowest in the brackish water reach, in accordance with Remane’s concept. An influence of the tributaries on zooplankton communities is suggested, directly by import or dilution of zooplankton communities or through changing environmental conditions.