A 7-year (March 1999eNovember 2005) monitoring program was developed in the Tagus estuary to study phytoplankton dynamics and several key controlling factors, namely nutrient content, light availability, atmospheric and hydrodynamic conditions (temperature, wind, rainfall, river flow, and salinity). Water was collected at four sampling sites on a monthly basis. Phytoplankton biomass, analyzed as Chl a, was moderate to low, when compared to other mesotidal estuaries: interannual average Chl a values ranged from 1.4 in winter to 8.0 mg L À1 in summer. A consistent seasonal pattern was observed, with a unimodal peak extending from late spring to summer. The phytoplankton community, as determined by biomarker pigment concentration using HPLC and CHEMTAX, was dominated by diatoms (57%), and included cryptophytes (23%), dinoflagellates (6.8%), chlorophytes (5.4%), euglenophytes (4.9%), and prasinophytes (2.6%). The method was capable of detecting phytoplankton taxa generally underestimated or overlooked when using standard microscopic techniques. Diatoms were the main bloom-formers in the summer Chl a maximum. A stepwise regression analysis showed that air temperature, river flow and irradiance explained 47% of the observed Chl a variance, illustrating the importance of climatic factors as driving forces for seasonal and interannual variability of phytoplankton.