The San Joaquin River, 330 miles (530 km) long, is the second-longest river in the U.S. state of California. The average unimpaired runoff of the main stem of the river at Millerton Reservoir is about 1,800,000 acre·ft (2.22 km3) per year. The San Joaquin and its eight major tributaries drain about 32,000 square miles (83,000 km2) of California's San Joaquin Valley. Water from the river is used to irrigate 1,500 square miles (3,900 km2) of highly productive farmland on the east side of the Central Valley where 200 kinds of produce are raised from oranges to cotton.

It originates high in the Sierra Nevada and drains most of the area from the southern border of Yosemite, south to Kings Canyon National Park, making it the second largest river drainage in the state. The San Joaquin River's tributaries include the Stanislaus River, Tuolumne River, Merced River, Calaveras River and Mokelumne River.

The river originates at three locations. The South Fork begins at Martha Lake at an elevation of 11,004 feet (3354 m). The Middle Fork begins at Thousand Island Lake and joins the South Fork north of Balloon Dome in the Ansel Adams Wilderness. The North Fork begins at an unnamed lake at 37°43′33″N 119°14′37″W / 37.72583°N 119.24361°W / 37.72583; -119.24361 that is at 3410 m (11190 ft) elevation and joins the Middle Fork east of Junction Butte at 37°31′56″N 119°10′55″W / 37.53222°N 119.18194°W / 37.53222; -119.18194.

The confluence passes through a narrow valley of which John Muir once said: "Certainly this Joaquin Canyon is the most remarkable in many ways of all I have entered." It eventually emerges from the foothills at what was once the town of Millerton, the location of Friant Dam since 1944, which forms Millerton Lake.

The river flows west to the Central Valley, where it is joined by the Sierra's other great rivers and then at Mendota Pool flows north to the Sacramento-San Joaquin Delta and then San Francisco Bay. With the exception of overflow and drain water along the North Fork of the Kings River, which meets the San Joaquin River at Mendota Pool, the San Joaquin River itself is the southern most river of the greater San Joaquin River watershed.

During some years, portions of the San Joaquin River (and some of its tributaries) will run dry as water is diverted from the river for urban or agricultural use. Though the agricultural drain water or urban waste water will be returned to the original channel downstream of the point of diversion, the water returned to the river is not of the same quality as the water found in the upper watersheds. In other places, such as at the confluence of the San Joaquin and Chowchilla Rivers near Dos Palos, California, the entire river has been diverted to man-made bypass channels, such as the Eastside Bypass. These bypass channels were originally designed to provide additional flood protection for local land owners. However, the levees on these bypass channels tended to be better designed and thus the main channel of the San Joaquin runs dry in some of these places.

The San Joaquin River meets the Sacramento River near the city of Antioch. Together they form the Sacramento-San Joaquin Delta, one of the largest estuaries in the United States. Before meeting the Sacramento River, the San Joaquin River has two distributary rivers, the Old River and the Middle River, both of which once were the main channels of the river. Due to the bend in the San Joaquin River channel at the head of the Old River, a significant portion of the San Joaquin River flow continues down the Old River instead of heading northward along the San Joaquin. This flow split causes problems for outmigrating salmon, as the flows along the Old River are eventually divided between the Old River, Middle River, and Grant Line Canal. Lower flows in these channels place the salmon in danger of predation and entrainment via agricultural diversions and urban drinking water exports. In response to this problem, the California Department of Water Resources and California Department of Fish and Game construct and manage temporary rock barriers at the head of the Old River in order to keep fish in the main channel of the San Joaquin River.

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