Water from the San Joaquin Delta, having chloride concentrations up to 3590 mg/L, has intruded fresh water aquifers underlying Stockton, California. Changes in chloride concentrations at depth within these aquifers were evaluated using sequential electromagnetic (EM) induction logs collected during 2004 through 2007 at seven multiple-well sites as deep as 268 m. Sequential EM logging is useful for identifying changes in groundwater quality through polyvinyl chloride-cased wells in intervals not screened by wells. These unscreened intervals represent more than 90% of the aquifer at the sites studied. Sequential EM logging suggested degrading groundwater quality in numerous thin intervals, typically between 1 and 7 m in thickness, especially in the northern part of the study area. Some of these intervals were unscreened by wells, and would not have been identified by traditional groundwater sample collection. Sequential logging also identified intervals with improving water quality—possibly due to groundwater management practices that have limited pumping and promoted artificial recharge. EM resistivity was correlated with chloride concentrations in sampled wells and in water from core material. Natural gamma log data were used to account for the effect of aquifer lithology on EM resistivity. Results of this study show that a sequential EM logging is useful for identifying and monitoring the movement of high-chloride water, having lower salinities and chloride concentrations than sea water, in aquifer intervals not screened by wells, and that increases in chloride in water from wells in the area are consistent with high-chloride water originating from the San Joaquin Delta rather than from the underlying saline aquifer.