Satellite observations of chlorophyll-a have been evaluated in the northern part of Caribbean Colombia but with little information in the southern part. We used twenty years of merged multi-satellite chlorophyll and wind information with fourteen years of sea surface temperature, (SST) and ten years of ocean currents. Missing Chl-a and SST data were estimated using the Data Interpolating Empirical Orthogonal Function (DINEOF) method. Results showed four regions with different seasonal patterns of Chl-a variability along the coast and there are other forcings that modulate the distribution of chlorophyll-a in the coastal areas of the southern part of the Caribbean Colombia (i.e SST, CDOM and Fluorescence Line Height). Also, the Gulf of Urabá (GU) region showed highest Chl-a concentrations along the annual cycle (1–7.5 mg m−3) with maximum values during the dry season (December-April); the Gulf of Morrosquillo (GM) region has the lowest Chl-a concentration with a seasonal maximum in the rainy season (May-November; ∼ 0.75 mg m−3); the Cartagena de Indias (CT) region with Chl-a concentrations > 0.75 mg m−3 along year and three seasonal maxima (January-February, June and September- December); and the Magdalena River mouth (MR) region were the Chl-a ranged between 0.5 and 1.5 mg m−3 showing similar annual maxima as in the CT zone, although the location of the high Chl-a areas were determined by changes in the orientation of the MR plume. This could suggest the occurrence of upwelling to the South of the MR during the dry and windy season, which could explain the seasonal maximum of Chl-a observed between January- February in MR and CT zones while rainy season in the GM, CT, and MR zones were synchronic with the annual maximum flow of Magdalena and Sinú rivers, suggesting that a nutrient supply by these rivers could support the high Chl-a concentrations observed.