In order to generate a conceptual model of seasonal distribution of water masses to Santa Marta bay, we identify, from main biotic and abiotic variables related to its water quality, patterns along the annual cycle. The model shows the major influence of the domestic residual water discharges during the rainy seasons (outwelling). These discharges explains the reduction of dissolved oxygen and water transparency and at the same times the increase of phosphorus and chlorophyll a concentrations. Although there is not stratification in the vertical nutrient distribution, there are differences in light distribution and consequently the primary productivity takes place mainly in the water column surface. The model shows that the outfall constitutes an important nutrient input and postulates as a hypothesis that the discharges will intensify the upwelling fertilization effect during the first half of the year, with low impact during the outwelling season due to water stratification.