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The Curonian Lagoon, the largest in Europe, suffers from nuisance cyanobacterial blooms during summer, probably triggered by unbalanced nutrient availability. However, nutrient delivery to this system was never analysed in detail. During 2012–2016, we analysed the monthly discharge, nutrient loads, and ecological stoichiometry at the closing section of the Nemunas River, the main nutrient source to the lagoon. The aim of this study was to investigate seasonal and annual variations of nitrogen (N), silica (Si), and phosphorous (P) with respect to discharge, climatic features, and historical trends. The nutrient loads varied yearly by up to 50% and their concentrations underwent strong seasonality, with summer N and Si limitation. The river discharge (16 ± 4 km³·yr⁻¹) was lower than the historical average (21.8 km³·yr⁻¹). Changes in agricultural practices resulted in similar N export from the river watershed compared to historical data (1986–2002), while sewage treatment plant improvements led to a ~60% decrease of P loads. This work contributes new data to the scattered available information on the most important nutrient source to the Curonian Lagoon. Further P reduction is needed to avoid unbalanced dissolved inorganic nitrogen and phosphorus (DIN:DIP~10) ecological stoichiometry in summer, which may stimulate undesired cyanobacterial blooms.