Coastal managers and policy-makers are concerned with tracking improvements to water quality linked to management changes. Long-term water quality data acquired from two wetland areas in the upper reaches of the Elkhorn Slough estuary in central California were analyzed for signatures of land restoration or water control structure management. Post-restoration averaged NO3, NH3, and PO4 concentrations were 50–70% less than before-restoration concentrations. Assessment of watershed-scale effects revealed that proximity of restoration to sampling locations had almost as strong an effect on water quality as the percentage of land restored relative to watershed size. Results also suggest that restoration of even 1% of an agriculturally intensive watershed such as that of the Elkhorn Slough may result in improvements to water quality. Finally, results indicate that tide gate function can dominate water quality in managed wetlands and must be carefully tracked and managed in the context of estuarine conservation targets.