The landscape is punctuated by 2,833 lakes larger than one hectare and an additional 1,600 ponds smaller than one hectare. The majority of the lakes are found in the eastern part of the country. Lithuania also has 758 rivers longer than ten kilometers. The largest river is the Nemunas (total length 917 kilometers), which originates in Belarus. The other larger waterways are the Neris (510 kilometers), Venta (346 kilometers), and Sesupe (298 kilometers) rivers. However, only 600 kilometers of Lithuania's rivers are navigable.

Water quality also is poor. The city of Kaunas, with a population of more than 400,000, still has no water purification plant. Only one-quarter of sewage-contaminated water in the republic is processed because cleaning facilities are not yet available. River and lake pollution also is a legacy of Soviet carelessness with the environment. The Kursiu Marios (Courland Lagoon), for example, separated from the Baltic Sea by a strip of high dunes and pine forests, is about 85 percent contaminated. Beaches in the Baltic resorts, such as the well-known vacation area of Palanga, are frequently closed for swimming because of contamination.