Cape Trafalgar has been highlighted as a hotspot of high chlorophyll concentrations, as well as a source of biomass for the Alborán Sea. It is located in an unique geographical framework between the Gulf of Cádiz (GoC), which is dominated by long-term seasonal variability, and the Strait of Gibraltar, which is mainly governed by short-term tidal variability. Furthermore, here bathymetry plays an important role in the upwelling of nutrient-rich waters. In order to study the spatial and temporal variability of chlorophyll-a in this region, 10 years of ocean colour observations using the MEdium Resolution Imaging Spectrometer (MERIS) were analysed through different approaches. An empirical orthogonal function decomposition distinguished two coastal zones with opposing phases that were analysed by wavelet methods in order to identify their temporal variability. In addition, to better understand the physical–biological interaction in these zones, the co-variation between chlorophyll-a and different environmental variables (wind, river discharge, and tidal current) was analysed. Zone 1, located on the GoC continental shelf, was characterised by a seasonal variability weakened by the influence of other environmental variables. Meanwhile, Zone 2, which represented the dynamics in Cape Trafalgar but did not show any clear pattern of variability, was strongly correlated with tidal current whose variability was probably determined by other drivers.