Protozoan communities at three beaches on the Cantabrian Sea were studied. Four stations along a transect of 150 m at each beach were chosen for this study. The following parameters were measured: temperature, pH, oxidation–reduction potential, dissolved oxygen, conductivity, salinity, nitrate, phosphate, granulometry and amount of organic matter. Four groups of protozoa (ciliates, non-dinoflagellate flagellates, dinoflagellates and sarcodines) were analysed for their abundance and diversity, as well as the influence of the measured parameters on the communities. Temperature, pH, and dissolved oxygen were the main factors responsible for seasonal differences. Temperature increased at the beginning of spring and summer, coinciding with growth of the protozoan community. Flagellates and dinoflagellates increased during spring and early summer. The amount of organic matter subsequently rose. The final step of this succession was the development of the ciliate community. A comparison between the same areas in 1989 and in the present study was carried out.