Using long-term records (~11 years) of salinity and 390 days of ADCP data, aspects of the estuary length and salinity flux were evaluated in Mobile Bay under a range of river discharge, tidal, and wind conditions. The temporal variability in the salinity structure was represented by the estuary length and showed a relationship of
with respect to river forcing, similar to values reported in San Francisco Bay and Delaware Bay. Local wind forcing was observed to play a role in modifying this relationship, in which estuary length responded asymmetrically to along-channel winds with up-estuary winds, reducing the estuary length. To further explore potential salinity transport changes associated with the wind, a 1D salinity flux was calculated using the ADCP and salinity profile data. River discharge was the main forcing condition driving seasonal changes in salinity flux. At shorter time scales, the wind became a dominant forcing condition and drove large changes in the salinity flux during low-discharge periods. At all discharge levels, down-estuary wind conditions enhanced the shear and subtidal exchange. During up-estuary wind conditions, the two-layer flow was inhibited and reduced the exchange. These results indicate that in a shallow microtidal system, wind can play a large role in modifying the estuary length on scales comparable to the spring–neap changes observed in other systems.