The Baltic Sea faces prolonged eutrophication due to nutrient pollution, with the Nemunas River regulating nutrient input via the Curonian Lagoon. In this study, we aimed to assess the seasonal variations and changes over the past two decades in nutrient concentrations within the Curonian Lagoon–Baltic Sea transitional zone, and to identify the main factors affecting these trends. We observed slightly reduced nutrient levels in the lagoon and the Klaipėda Strait and increased nitrogen loadings in the Baltic Sea nearshore over time. Between 2007 and 2009, the average total nitrogen (TN) concentrations in the Klaipeda Strait and the Baltic Sea were 1.60 ± 0.25 and 0.54 ± 0.04 mg/L, respectively, while the average total phosphorus (TP) concentrations in the Klaipeda Strait and the Baltic Sea were 0.061 ± 0.04 and 0.03 ± 0.01 mg/L, respectively. Between 2018 and 2020, TN concentrations in the Strait and the Sea were 1.2 ± 0.36 and 0.65 ± 0.32 mg/L, respectively, while the average TP concentrations in the Klaipeda Strait and the Baltic Sea were 0.025 ± 0.002 and 0.021 ± 0.002 mg/L, respectively. The average annual amount of TN and TP entering the Curonian Lagoon from the sea was 2736 t and 162 t, respectively. Significantly higher nutrient influx to the Baltic Sea was recorded reaching 32,302 t for TN and 1278 t for TP. Nutrient concentrations correlated with water temperature, salinity, and dissolved oxygen, influenced by seasonal runoff patterns and climate change. Over time, there have been noticeable shifts in environmental conditions, including rising temperatures, decreasing oxygen levels, salinity changes, increased evaporation, and reduced precipitation.