The San Joaquin River is the longest river in Central California, and the second most endangered river in the country. But because of dams, levees, and water diversion, over 100 miles of the river has been dry for 50 years. Sacramento – The San Joaquin River is second only to the Apalachicola, Chattahoochee and Flint rivers basin in Alabama, Georgia, and Florida as a seriously endangered river in this country.