In the Bay of Algeciras (BA), intensive urban and industrial activityis underway, which is potentially responsible for the release of significant quantities of nutrients. However, the assessment of the impact of these discharges is complex. Nutrient concentration in the surface layer is per se strongly variable due to the variability associated with the upwelling of nutrient-enriched deep Mediterranean water (MW), which in turn is regulated by atmospheric forcing. The aim of this study is to determine the effects of changes in the upwelling intensity on the load of nitrate and phosphate in the BA and to appraise their impact on chlorophyll a variability. Based on this analysis, the possible influence of the nutrients released from land-based sources is indirectly inferred. Data and samples collected during nine research cruises carried out in different seasonal cycle periods between 2010 and 2015 in the BA were analysed. The vertical variation of temperature and salinity indicates that the MW upwelling was favoured in spring, as occurred in other coastal areas of the northern Alboran Sea. However, principal component analysis conducted on physical and chemical data reveals that shifts in nutrients and chlorophyll a in the euphotic layer are poorly explained by changes in the upwelling intensity. Furthermore, during some of these research surveys (particularly in summer), chlorophyll a concentrations were higher in the BA as compared to a nearby coastal area also affected by MW upwelling. Scarce information about land-based pollution sources precludes quantitative analysis of the impact of nutrient loads on water quality; however, the available data suggest that the main source of allochthanous inorganic nitrogen over the period 2010-2015 in the BA was nitrate. Therefore, it is reasonable to hypothesize that the high concentrations of nitrate and chlorophyll a in BA in summer are a consequence of those discharges. Our study highlights the need of more exhaustive inventories of sewage and river discharges to adequately rate their impact in the BA.