Regular samples at nine stations ranging from fresh water to fully marine conditions in the Forth Estuary and Firth, on the East coast of Scotland, allow a description of the community structure, composition and distribution of the zooplankton over an eighteen month period. A transition gradient in the occurrence of species along the length of the estuary was clearly identified that could be linked to salinity and hydrographic features using both traditional and nonparametric techniques. The fauna included both resident estuarine and incursive marine populations, having strong seasonal components of variation.Calanoid copepods dominated the estuary, with Eurytemora and several Acarfia species present, independent from analogous populations to seaward. The data reflected distinct seasonal episodes of predatory dominance, resulting in the temporary but complete absence of grazers in the lower estuary. In the middle and upper estuaries there was an apparent complete dislinkage between the phytoplankton levels and the zooplankton. It is hypothesised that the zooplankton of the upper and middle estuaries were dependant not upon phytoplankton but upon either anthropogenic inputs of distillery waste and sewage, or the microphytobenthos.