Competition for California's limited water resources has become increasingly vigorous in recent years. Agricultural and domestic use compete with recreational requirements and legally mandated flows to protect native species. This has led to a need for a reliable determination of the net flow of fresh water into the San Francisco Bay. This requires measuring small net flows in the presence of large tidal flows. We have studied the errors on net flow determined from such measurements, with one of the principal flow channels in the Sacramento-San Joaquin River Delta used as an illustrative case study. Continuous monitoring of average channel discharge requires the use of a well calibrated index velocity. We find that the principal error in the determination of net flow lies in the calibration of the index velocity. In our case study, present technology allows the net discharge under conditions of lowest flow to be measured to measured to a precision of 1/2 % of the peak tidal flow.