Physical-chemical variables, phytoplankton biomass, species composition and photosynthesisirradiance (P-I) parameters were analysed during 1 year in the Santo André Lagoon, Southwest Portugal - a land-locked coastal ecosystem with temporary connections with the sea. When the lagoon stayed closed the observed phytoplankton blooms were mainly caused by Prorocentrum minimum, a potentially toxic dinoflagellate. It was dominant during most of the year bur the seawater inflow to the lagoon triggered a decrease in phytoplankton biomass and an abrupt shift in species composition. The maximum photosynthetic rate (Pmax) ranged from 2.0 to 22.5 mg C (mg chlorophyll a)-1 h-1 and the light saturation index (Ik), ranged from 5.2 to 335.0 μE m-2s-1, with winter minima and summer maxima. Pmax and Ik were both positively correlated to temperature. Abundance of P. minimum was associated with high nitrate concentrations whereas diatoms appear when ammonium, salinity and wind velocity are high. A mathematical model to describe photosynthetic rate as a function of irradiance and temperature [P (I, t)] was applied to the samples in which P. minimum was the dominant species.