Waterways have been extremely important in the development on Värska. During many centuries, Värska and the whole coast of Lake Pskov were connected with Tartu and other settlements by waterways. Ships were built in many villages, including Värska.
Vessel traffic got its first hit from the Tartu-Pechory railroad that was opened in 1931. Before that, all of the cargo transport as well as passenger transport had moved through the port of Värska. Later the road traffic become the dominant means of transport and the port was neglected.
Nowadays people are looking for new ways to spend their time and water tourism is an increasing activity. Värska harbor, built in 2020, offers docking for different types of vessels and is equipped with services and technical infrastructure. There is a parking lot, a patent slip, a floating dock, café and restrooms. The port is complemented by a 300 m promenade along the coastline of the Värska Bay. The bay is suitable for cruising and water sports, but attention must be paid to the border regime.