Anthropogenic (aquaculture) changes in environment nutrient concentrations may affect phytoplankton (biomass and taxa composition) in marine coastal waters off the Chilean Patagonia. The effects of adding nitrate (NO3 (-)) to natural phytoplankton assemblages were evaluated considering biomass, cell abundance, and taxonomic composition. Microcosm experiments were performed in the spring, summer, and winter in the Comau Fjord located in Subantarctic Patagonia. At the end of the experiments, NO3 (-) decreased rapidly and was undetectable in treatments, indicating a strong NO3 (-) deficiency associated with an exponential increase in Chl-a concentrations, particulate organic nitrogen, and carbon in these treatments. Moreover, given the depleted nitrate concentrations of the spring and summer experiments, the micro-phytoplankton taxa structure shifted from mixed diatom and dinoflagellate assemblages (Ceratium spp., Dinophysis spp., Coscinodiscus sp., Rhizosolenia pungens) to assemblages dominated by blooms of the classic chain-forming diatoms found in temperate and cold waters such as Chaetoceros spp., Skeletonema spp., and Thalassiosira spp. Thus, nitrogen sources (i.e., nitrate, ammonia) may influence phytoplankton abundance and biomass accumulation dynamics in the northern section of Patagonia. It also emphasizes the importance of diatom taxa in regards to the short-term response of phytoplankton to changing environmental nutrient conditions due to natural (decreasing freshwater stream flow) and anthropogenic (aquaculture) events. This situation may be one of the future scenarios in the Patagonian fjords, thus stressing the needs for active environmental monitoring and impact assessment.