The creation of residual flows in estuaries is examined using acoustic Doppler current profiler data sets from northern San Francisco Bay. The data sets are analyzed using principal component analysis to examine the temporal variability of the flows which create the residual circulation. It is seen that in this periodically and partially stratified estuary the residual flows are created through a series of pulses with strong variability at the 24‐hour timescale, through the interaction of shear, stratification and mixing. This interaction is captured through the use of a dimensionless number, the horizontal Richardson number (Ri_x), which is developed to examine the local balance between the stratifying and destratifying forces at the tidal timescale. It is seen that Ri_x is a valuable parameter in predicting the onset of the residual‐creating events, with a threshold value of ≈3 on ebb tides. This critical value is argued to be a threshold, above which the stratification and shear flow create a feedback effect, each further intensifying the other. This feedback results in a highly variable exchange flow which creates the estuarine residual in intermittent pulses rather than as a steady flow. Although typically attributed to baroclinic forcing, an argument is made that these pulses of residual‐creating exchange flow could be created by barotropic forcing in the presence of variable stratification which is asymmetric between flood and ebb tides. This result poses a great challenge for turbulence modeling, as the timing and magnitude of stratification and shear must be correctly simulated on the tidal timescale in order to reproduce the effects seen in the data sets presented.