The spatial patterns of chlorophyll a and bacteria were assessed in a temperate Atlantic tidal estuary during seasonal surveys, as well as in consecutive summer spring and neap tides. A box model approach was used to better understand spatial and temporal dynamics of these key estuarine descriptors. The Lima estuary (NW Portugal) was divided into boxes controlled by salinity and freshwater discharge and balance equations were derived for each variable, enabling the calculation of horizontal and vertical fluxes of plankton and, therefore, production or consumption rates. Chlorophyll a tended to burst within the oligohaline zone, whereas higher counts of bacteria were found in the mesohaline stretch. Whenever the water column was stratified, similar tide-independent trends were found for chlorophyll a and bacterial fluxes, with net growth in the upper less saline boxes, and consumption beneath the halocline. In the non-stratified upper estuary, other controls emerged for chlorophyll a and bacteria, such as nitrogen and carbon inputs, respectively. The presented results show that, while tidal hydrodynamics influenced plankton variability, production/consumption rates resulted from the interaction of additional factors, namely estuarine geomorphological characteristics and nutrient inputs. In complex estuarine systems, the rather simple box model approach remains a useful tool in the task of understanding the coupling between hydrodynamics and the behavior of plankton, emerging as a contribution toward the management of estuarine systems.