Physical and chemical parameters were measured in a mostly freshwater estuarine lagoon in the SE Baltic. Present paper demonstrates an attempt to trace the sources and analyse the seasonal and spatial patterns of distribution of POC, DIC and DOC in the Curonian lagoon mostly by the isotopic content in different forms of carbon. Samples were collected in 2012-2014 in 9 stations in the Curonian lagoon including riverine and marine input/output stations. Riverine inputs and summarizing outflow to the Baltic sea locations (Nemunas river delta and Klaipeda channel stations were sampled monthly, while POC, DIC and DOC samples in other stations were collected on a seasonal basis. The observed results allow easily differentiate between estuarine and riverine POM samples, while the differences in DOC δ13C content between sampling stations were found to be not statistically reliable. The high biological productivity of the Nemunas river along with the minor contribution of the Baltic Sea inflows to the overall hydrodynamics of the lagoon explain similarity of content between riverine and estuarine material in the spring and autumn. However, the δ13C content of DIC and DOC could serve as indicator of external inputs only in connection with seasonal water residence variations.