BACKGROUND: A fundamental step in characterizing marine planktonic communities is the knowledge of the variability of their biomass and production, in order to assess the flux of matter through the food web and estimate the fate of this energy. The zooplankton assemblage's dynamics of the Mondego estuary (Portugal) have been extensively characterized, but none have focused on biomass and secondary production. In the present study, zooplankton biomass and secondary production were investigated with a seasonal basis in a fixed station, located at the mouth of the Mondego estuary (Portugal), with emphasis on the copepod community. In order to study the influence of physical processes operating at different temporal scales, sub-surface and near-bottom samples were collected every 2 h in diel and tidal cycles, over neap tides. RESULTS: Copepodsdominated the biomass during spring (0.585 ± 0.671 mg C m-3),summer (0.287 ± 0.383 mg C m-3), andwinter (0.221 ± 0.128 mg C m-3).Lower observed biomass values were probably due to the higher mesh size used in comparison to previous studies in other estuarine systems. No differences were detected between seasons in total zooplankton biomass. Concerning diel cycle, significant variation occurred mainly in spring and winter, with substantially higher biomass values being registered at night for both the surface and bottom. Moreover, copepod biomass was consistently higher at the bottom during winter. In this season, bottom samples presented higher copepod biomass both at ebb and flood tides. From the GLM analyses run for each season, chlorophyll a, diel phase, and depth were significant factors. CONCLUSIONS: Theconsiderable complexity in the processes structuring the dynamics and composition of biomass and production rates has been shown. Our results demonstrated that along spring and winter, secondary production varied according to diel phase and depth. In winter, night and bottom samples revealed consistently higher daily secondary production rates. From this, it is possible to conclude that local factors (river flow, predation, food limitation) regulate the seasonal variations in zooplankton biomass and production in the Mondego estuary.