Three water quality monitoring sites have been selected on the San Joaquin River. Site G (San Joaquin River at Fremont Ford) is located downstream of Salt Slough and upstream of the Mud Slough (north) confluence. This site is presently impacted by agricultural subsurface drainage. With the use of the Grassland Bypass, drainage will be discharged to the San Joaquin River downstream of this site. Monitoring at this site will allow the assessment of the assumptions made regarding water quality benefits as a result of the use of the Grassland Bypass. Water quality data taken from this site will be used, with biota data, to study recovery of a site formerly impacted by drainage.

Site H (San Joaquin River at Hills Ferry) is located downstream of the Mud Slough (north) confluence but upstream of the Merced River confluence. This site will provide data by which to evaluate water quality impacts to the San Joaquin River and for compliance with water quality objectives.

Sites N (San Joaquin River at Crows Landing) is located downstream of the Merced River confluence. This site is a CVRWQCB compliance point.