Bathymetric data of Lithuanian inland waters include information on the largest Lithuanian lakes, ponds, Kaunas and Curonian Lagoons and part of the sea coast depths. Data were prepared by systematization and vectorization of the Natural Research Center, Institute of Geology and Geography Climate and Water Systems Sector, Inland Waterways Directorate, Environmental Protection Agency, Natural Heritage Fund, Samogitian National Park Directorate, SE GIS-Center, Klaipeda University Baltic Sea Environmental Research and Planning Institute (Aleksandras Stulginskis and Lithuanian universities of educology) (bathymetric plans, schemes). Systematization, vectorization and data set development of the material was performed by SE GIS-Centras.