Cape Ghir (~31°N), in the Canary Current System, is an area of permanent coastal upwelling with maximum intensity in summer-autumn, when a strong across-shore thermal gradient and increased mesoscale activity are present. The effects of spatial (cross-shore transect with 7 stations) and temporal (5 dates: from December 2008 to October 2009) variations in upwelling conditions on the structure of planktonic communities (functional groups, size and taxa composition, abundance and carbon biomass) were investigated. Multivariate analysis of the environmental variables enabled both spatial separation of the stations, based primarily on differences in nutrient concentration, and a temporal distinction of upwelling phases, based mostly on differences in sea surface temperature and number of days favourable to upwelling. These clusters were also representative of the time-space variability in the planktonic communities, suggesting that upwelling conditions directly influence their structure. For most of the cruises, the microplankton (mainly diatoms and auto/mixotrophic dinoflagellates) made the highest contributions to photoautotrophic carbon (C) biomass but the nanoplankton (mainly flagellates and dinoflagellates) made the largest contributions to total chlorophyll-a (Chl-a). Mean heterotrophic:autotrophic biomass ratios (from pico-to microplankton during three cruises) were mostly ≤1 (normal pyramid), as expected for productive coastal areas, only when the contribution of mixotrophy was considered. A mixed composition of functional groups of autotrophs/mixotrophs in the coastal and coastal transition zones off C. Ghir is probably the result of the nutrient contents in the upwelled waters since potential silicate or nitrate limitation together with a relatively high C:Chl-a in the micro-phytoplankton were detected during some of the cruises. Temporal changes in diatom taxa with different nutrient requirements also suggested a strong influence of nutrients. The comparatively lower nutrient contents in the upwelled waters off Cape Ghir are linked to the regional circulation patterns, a relatively narrow shelf (lower residence time of the upwelled waters), a higher level of mesoscale activity, and with weak to moderate wind intensities for most part of the year.