Time series of current velocity profiles and thermistor chains were obtained throughout a cross-bay transect for ~90 days for the purpose of comparing observed wind-driven stratified flows to theory. This study concentrates on the synoptic scale wind and its influence on the bay’s circulation. The maximum water column stratification was 3–4 °C/m throughout the deployment and influenced wind-driven flows. Low-pass filtered flows showed more complicated structures than those expected from theory: a depth-dependent recirculating structure with the along-bay flow over one half of the transect moving in opposite direction to the other half. Analysis of complex empirical orthogonal functions indicated that the first six modes explained 80 % of the flow variability. Therefore, there was no predominantly energetic mode of variability. All modes exhibited a rich spatial structure with vertical and lateral variations. For all modes there was vertically sheared bidirectional flow, as expected from theory, with the largest eigenvector (mode value) asymmetrically influenced by Earth’s rotation and advection of momentum.