Moored observations are used to investigate the seasonal change in vertical structure of the cross-shelf circulation at a midshelf location in the northern California Current System. A streamwise–normal coordinate system is employed to eliminate meander- and eddy-induced biases in the cross-shelf flow that are unaccounted for with an alternative, commonly applied approach. The resulting flow structure develops an organized pattern midway through the upwelling season. In particular, under upwelling-favorable conditions an onshore return layer occurs just beneath the offshore surface flow, and a third offshore-directed layer exists at depth that does not appear to satisfy Ekman dynamics (to within 9 m of the bottom). Both subsurface layers strengthen in time over the upwelling season. Mechanisms to explain the mean structure are evaluated, and it is suggested that the timing of the development and strengthening of both the interior onshore return flow and the offshore near-bottom layer are consistent with the seasonally changing direction and magnitude of the large-scale alongshelf sea level gradient. The change to a poleward sea level gradient initiates a seasonal relaxation of upwelled isopycnals that likely leads to the near-bottom flow. Late-season enhancement of the interior onshore return flow is related to the alongshelf surface wind stress but appears to form as a consequence of offshore transport in the near-bottom layer and the need to satisfy coastal mass balance.