The main suppliers of sedimentary matter into the large coastal freshwater lagoon of the southeastern Baltic (Curonian Lagoon) are the Neman River including the sleeves Atmata, Skirvytė and Razliv, as well as Matrosovka and Deima rivers. Large catchment area of the rivers densely populated and characterized by intensive industrial and agricultural activities, which are regarded as potential suppliers of biogenic and chemical elements. Elevated amounts of biogenic components (nitrogen and phosphorus) as well as arsenic recorded in sediments from the river mouth areas suggest serious contribution of anthropogenic activities (use of fertilizers and pesticides in the agricultural activities) on the general sediment quality in the investigated area. Newly obtained data clarify the patterns of biogenic and trace element distribution in sediments located in close vicinity of potential pollution sources.