SJAFCA's mission is to reduce and manage flood risk within most of San Joaquin County. It is working to fulfill this mission in part by planning, designing, financing and constructing flood risk reduction projects and funding operations and maintenance of existing projects. 

The Agency's Strategic Plan its approach, decisions, investments and actions to reduce flood risk. Ongoing projects include, but are not limited to:

• Smith Canal Gate Project
• Lower San Joaquin River Project
• Mossdale Tract
• Lower San Joaquin River Feasibility Study Phases I & II
• Lower San Joaquin River & Delta South Regional Flood Management Planning
• FEMA Levee Accreditation Projects
• Aquatic Weed Control Program