San Joaquin, California is located in the southern part of the state's Central Valley. The region experiences a Mediterranean climate, characterized by hot, dry summers and mild, wet winters. Summers in San Joaquin are typically hot and can see temperatures reaching into the triple digits, while winters are mild with average temperatures in the 50s. Rainfall is limited, with most precipitation occurring between November and March.

Hydrologically, the San Joaquin area is influenced by the San Joaquin River, which flows through the region. The river serves as a vital water source for agriculture, industry, and residential use. The river also supports various aquatic species and habitats. However, due to water diversion for agricultural purposes, the river's flow has been significantly reduced in recent decades.

San Joaquin offers several outdoor recreation opportunities. The nearby Sierra Nevada mountains provide opportunities for hiking, camping, and exploring the wilderness. The region also boasts numerous parks and lakes, such as Woodward Regional Park and Millerton Lake, where visitors can enjoy activities like boating, fishing, and picnicking. Additionally, the San Joaquin River National Wildlife Refuge offers opportunities for bird-watching and wildlife observation.