The spatial and temporal variability of phytoplankton abundance (in terms of chlorophyll a and cell number), inorganic nitrogen, suspended particulate matter (SPM), and light availability was determined throughout one year in the Tagus estuary, Portugal. Chlorophyll a concentrations showed a strong seasonal variation with values ranging from 1 to 32 g l–1(average 5.4 g l–1). Chlorophyll patterns were unimodal for sites 1, 2, and 3 and bimodal for site 4. Diatoms and cryptophytes were, throughout the year, the dominant groups in this shallow and unstratified estuarine system. Nitrate concentrations were seasonally related to river flow and ammonium concentrations spatially related to sources of sewage input. Lower river inputs and long water residence times during summer initially promoted the accumulation of phytoplankton, but the resulting low dissolved inorganic nitrogen (DIN) concentrations lead to limitation of phytoplankton growth. Chlorophyll a and DIN values obtained in the present study were comparable to those reported 20 years ago for the Tagus estuary.