The ciliate and flagellate protozooplankton of the Clyde Estuary and Loch Striven were investigated over a 12 month period in 1990. There were distinct differences in the patterns of occurrence and numbers of the Protozoa in the two brackish locations, attributable to different physical and chemical conditions. Phototrophic flagellate numbers were higher in Loch Striven, where overall chlorophyll a concentrations were also higher. In contrast heterotrophic flagellate densities were higher in the Clyde and were abundant throughout the year, while in Loch Striven they showed a distinct seasonal pattern with peak numbers occurring in the summer. Heterotrophic dinoflagellates were periodically very abundant, particularly in Loch Striven and the lower Clyde. The ciliate communities showed marked differences in species composition and higher numbers occurred in the Clyde compared to Loch Striven. Tintinnid ciliates formed a regular component of the community in Loch Striven, but were less common in the Clyde. However, aloricate ciliates, particularly oligotrichs and very small bactivorous ciliates (< 20 μm) dominated the ciliate assemblage. Apart from Laboea very few of the oligotrichs contained plastids, and were therefore not practising mixotrophy. In both systems the microbial plankton is largely dependent on allochthonous carbon. High turbidity, particularly in the Clyde resulted in low concentrations of chlorophyll a and a low incidence of mixotrophy among ciliates.