Ecosystem management and decision making process are dependent of a good knowledge of ecosystem functioning. Conceptual models allow knowledge organization through representation of relationships between variables and processes, facilitating management decisions. In this study, spatial and temporal characterization of key environmental variables, as well as relationships between them, was studied aiming the design of a conceptual model of the Douro estuary. This temperate mesotidal estuary is limited upstream by a hydroelectric power dam that controls freshwater inflow and prevents the propagation of the tide upstream, which, in turn, influences water circulation and biogeochemical dynamics of the system. During one year, from December 2002 to December 2003, water column data were collected monthly at 10 stations along the estuary, during ebb and flood tides. Spatial and temporal variability of water column salinity, temperature, nutrients, phytoplankton biomass, total particulate matter (TPM), phytoplankton primary production (PP), faecal coliform bacteria (FC) and community respiration (CR) were analysed. Salinity stratification was assessed by means of the Estuary Number (Ne) and variation of this index as well as other key characteristics with river flow was analysed. Freshwater discharge controlled salinity stratification and freshwater residence time. Ne indicated that the Douro was stratified for river flows <300 m 3 s −1, and freshwater residence time was >1 day for the same conditions. A decaying exponential relationship between PP and river flow was found, whereas nitrate and TPM increased logarithmically and linearly, respectively, with river flow. Regarding spatial distribution, nitrate and PP decreased downstream, showing that the river was a source of nutrients and phytoplankton, while the opposite trend was found for TPM, FC, ammonium and CR. The latter increase was probably due to untreated sewage discharge in the urbanized middle and lower estuarine stretches. Reduction of nitrate coming from the watershed and of bacterial contamination in the urban stretches of this highly modified water body, according to the European Water Framework Directive, emerges as the main water quality issues for this estuarine ecosystem.