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Coupled three-dimensional hydrodynamic and ecological numerical simulations were used to investigate the role of transport, stagnation zones and dispersion on inter-annual blooms of the diatom Aulacoseira sp. in the vicinity of the drinking water intakes of the Buenos Aires city (Argentina) in the upper Río de la Plata. Three different summer events were analyzed. First, a mild biomass bloom year (2006–2007), second, a high biomass bloom year (2007–2008) and third, a “normal” no bloom year (2009–2010). Simulated water height, water temperature, suspended solids and chlorophyll concentrations patterns compared well with field data. Results revealed that the advection of phytoplankton cells via inflows to the Río de la Plata triggered Aulacoseira sp. blooms in the domain. In addition, excessive growth observed near the drinking water intakes, along the Argentinean margin, were associated with long …