The composition in terms of protozoan functional groups of three sublittoral areas (Castro Urdiales, Santoña and Isla) in the Cantabrian Sea was analysed. The different protozoan species were identified, and their density and biomass was measured. The pigmented protozoa were the most important group in the three areas throughout the year, followed by the bacterivores in Castro Urdiales and Santoña, and the non-selectives in Isla. Bacterivores constituted the most significant group in terms of biomass, after which came that of non-selectives. The parameters with the strongest influence on distribution in functional groups (respect to biomass) were pH, phosphate, organic matter and bacterial biomass, other significant factors being salinity, nitrate and mean grain size. Functional groups expressed as number of species were affected principally by phosphate, pH and, to a lesser extent, temperature and salinity. Statistical analysis using the present data, data regarding functional groups from previous studies in the same areas, and data from other areas, indicate that marine areas show similar characteristics. In the areas covered by the present study, there was a decrease in the number of algivore species and a rise in non-selective species, while bacterivores and pigmented protozoa maintained similar values. In comparison, freshwater areas showed noticeably lower percentages of algivore species and a significantly higher number of bacterivore species.