A long-term study (monthly sampling, 1992 to 2007) was conducted in the surf zone of Cassino Beach, Southern Brazil, in order to detect possible natural and/or anthropogenic disturbances. Surface water temperature (6-29°C) was the only parameter with predictable seasonal variation; salinity (14-38) was inversely related to rainfall (3.1-485.2 mm month −1 ) and low values followed extreme precipitation periods in and 2002/2003. Asterionellopsis glacialis and chlorophyll a presented high concentrations and peak frequency until 1998, when an intense mud deposition occurred with concomitant extreme rainfall. It affected the surf zone and beach, changing the hydrology and dissolved inorganic nutrient availability. Six phytoplankton species groups were recognized with distinct responses to this mud deposition. We conclude that large-scale climatic changes, like El Niño Southern Oscillation, in conjunction with human activities significantly altered the phytoplankton ecology of the highly dynamic Cassino Beach surf zone.