The pelagic metabolism of the Douro estuary (Portugal) and the factors influencing primary production (PP) and community respiration (CR) in this system were studied during an annual cycle (December 2002eDecember 2003. Sampling surveys were conducted twice a month during ebb and flood spring tides and water samples were collected for PP and CR assessments at three stations along the estuary (lower, middle and upper stretches). During the study period, PP values were in the range of 4.7e1878.5 mg C m ÿ2 d ÿ1 (average, 319.9 mg C m ÿ2 d ÿ1 ). River discharge controlled phytoplankton biomass inputs into the estuary as well as residence time. A decreasing trend in water column PP from the upper to the lower estuary related to higher nitrogen concentrations and phytoplankton biomass from riverine origin was observed. An inverse trend was found for CR, i.e., higher values were found in the lower, more urbanized stretch. During the study period, averaged CR values reached 1154 mg C m ÿ2 d ÿ1 . In general, heterotrophy dominated the entire estuary, except in the upper stretch from May through July, when increased PP, but also lower CR values were recorded. A positive correlation between chlorophyll a and P max was found which is unusual in coastal ecosystems, where a decreasing trend of the P/B ratio as a function of net primary production is generally observed. This could be explained by the relatively low phytoplankton biomass, preventing intraspecific competition from lowering photosynthetic capacity, on one hand, and the physiology of phytoplankton related to their origin in a semi-lotic (reservoir) ecosystem. No significant differences between tides were observed for all variables, except for the water light extinction coefficient (k) values, reflecting higher turbidity during the ebb.