Thermohaline density stratification may significantly alter the classic near-bottom logarithmic velocity profile in many weak to moderately energetic, partially mixed estuaries. Results from Eckernf¿rde Bay suggest fits to log profiles which neglect thermohaline stratification may lead to overestimates of bottom stress and roughness of the order of 130% and 600%, respectively. Measurements of velocity obtained at four heights within 1 m of the seabed are input to theoretical models for velocity shear derived via dimensional arguments for the overlap layer. Previous investigators applying dimensional arguments to thermohaline stratification in estuaries have assumed buoyancy flux to be independent of height within the overlap layer. This may be a poor assumption since there is no significant source or sink of thermohaline buoyancy at the sediment-water interface. In this paper, dimensional arguments which do not assume constant buoyancy flux are used to reduce estimates of the drag coefficient and bottom roughness to below the unreasonably high values predicted by simple log profiles. Formulations assuming very weak and relatively strong stratification are applied, and estimates of buoyancy frequency derived from fits to velocity profiles are compared with independent estimates of stratification. Estimates of bottom stress and roughness derived from velocity profiles are also found to be sensitive to fluid acceleration, uncertainties in instrument settling, and limitations in current meter accuracy, but these latter effects appear secondary in Eckernf¿rde Bay to the impacts of thermohaline stratification.¿ 1997 American Geophysical Union