The Curonian Lagoon is a unique system that is a temporary reservoir of water, accumulating about 62% of the suspended solids in the river runoff. The average activity of plutonium in the suspended particulate matter in the water of the Neris River was 0.26±0.02 Bq/kg, and the activity of 137Cs ranged from 23±8 to 49±12 Bq/kg. The average 137Cs flux to the Curonian Lagoon in the particulate and dissolved species was estimated to be (78±61) × 109 Bq/year. Preliminary estimates indicate that the annual input of 239,240Pu from the Neman River into the Curonian Lagoon is about 0.9 GBq, of which 0.56 GBq accumulates in the sediment of the lagoon.