Abstract From July 2001 to May 2005, seawater samples were collected once a week at a fixed station in Lisbon bay (38°41′N, 09°24′W) in order to describe the ecological dynamics of the coccolithophore community. The seasonal and interannual distribution patterns of the different species and their relationships with environmental parameters are addressed. The present work aimed to identify potential proxies for different local water bodies and environmental conditions. Throughout the period of study, the upwelling events were weak and progressively more persistent. High sea surface temperatures (SST) were observed earlier in the year; summers and winters were gradually warmer and colder, respectively. Salinity variations reflected the different weather conditions as they are strongly influenced by rainfall and thus by the Tagus river flow. The extended periods of weak upwelling and the overall increase in SST resulted in the development of phytoplankton populations as measured by chlorophyll a. However, the persistence of the upwelling, and thus shorter convergence periods, favoured other phytoplankton groups than coccolithophore populations as these decreased towards the end of the sampling period. The annual structure of the coccolithophore assemblage showed a pronounced and recurrent seasonal variability, mainly related with the intensity and persistence of upwelling. The highest cell densities were recorded from spring to autumn. An overall preference by most species for mature upwelled waters and low turbulent conditions was observed associated with high temperatures and salinities, although the species develop in different windows with mismatching maxima. The coccolithophores observed were capable of withstanding coastal processes such as turbulence and were well adapted to an environment rich in nutrients provided by both continental runoff and upwelling. The consistency of the results enabled local oceanographic tracers to be defined. Emiliania huxleyi and Gephyrocapsa species can be used as proxies of surface productivity waters during spring and summer while Coccolithus pelagicus indicates the presence of upwelling fronts. Calcidiscus leptoporus is a tracer of the convergence of subtropical oceanic waters onto the shelf, during winter while Coronosphaera mediterranea, Syracosphaera pulchra, Helicosphaera carteri and Rhabdosphaera clavigera revealed the presence of those waters during the short period that characterized the transition from upwelling to downwelling seasons.