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Chlorophyll-a (chla) is an important parameter to assess water quality in lakes and reservoirs, since it is a proxy for phytoplankton biomass and primary production. The increasing availability of data with high spatial and temporal resolution allows assessing short-term dynamics and small-scale variations of chla within larger water bodies. In freshwater reservoirs, the nutrient concentrations and the physical conditions that control phytoplankton growth vary along their longitudinal extend. Here, we analyze how the flow paths of the inflowing river water into density-stratified reservoirs affect the vertical and longitudinal distribution of nutrients and chla. We combine spatially resolved and high-frequency measurements of chla from satellite remote sensing and in-situ sensors, with numerical simulations using a three-dimensional hydrodynamic model to assess the influence of density currents on chla dynamics along a subtropical drinking water reservoir in the south of Brazil. Chla did not have pronounced seasonal dynamics (4.9 ± 1.2 µg L−1, at the continuous measurement station); instead, spatial variability along the reservoir was more pronounced (4.4 ± 2.1 µg L−1, all monitored points within the euphotic zone). Most of the nutrients from the inflowing river were consumed in the upstream region, and phytoplankton in the lacustrine zone depended on internal loading. Temporal variability was observed only in the upstream region, and phytoplankton produced in that area was transported downstream by density currents, resulting in large concentrations of chla below the euphotic zone. The results of a hydrodynamic model that simulates the present state are in good agreement with the observations. Two simulated scenarios, where the density current patterns were altered, resulted only in slight variations in density currents, indicating that the influence of the main inflow was of minor relevance in chla concentrations in downstream regions of the reservoir. Our results highlight the importance of two-dimensional hydrodynamic processes in regulating phytoplankton dynamics in reservoirs.