The Napa River is one of only three navigable rivers in California. From the City of Napa southward, the River is subject to tides and widens into broad marshes. This reach is best explored by canoe, kayak and small motor boats. The river empties into San Pablo Bay, and there are marinas for bay- and ocean-going boats.

In the Lake District east of Napa Valley, Lake Berryessa provides a variety of water-based recreation, including water skiing, fishing, swimming and houseboat rental.