Circulation in typical fjords is characterized by a shallow brackish layer at the surface over a deep long and narrow saltwater column. This surface layer is responsible for the outflow of water from the fjord and is important for flushing of the basin and water quality maintenance. The vertical structure of circulation and transport is known to be easily disrupted, and we postulate that the stability of fjordal circulation may also be vulnerable to impacts from anthropogenic alterations, such as floating structures, which could constrict the mixing and transport in the upper layers of the water column. First, using simplified fjord geometry and a three-dimensional finite volume coastal ocean model (FVCOM), a baseline examination of tidally averaged current profiles in basins with and without sills is presented. The response, varying from a partially mixed estuary regime to classical fjord conditions matches many fjord-like basins such as those in Puget Sound, Washington. The effect of surface obstruction on tidally averaged currents and residence times was then examined by incorporation of a narrow block in the surface layer of the model across the width of the simplified fjord channel such that normal velocity in the horizontal direction was forced to zero. This block approximated the presence of a floating bridge and was further tested using the geometry of Hood Canal, a fjordal sub-basin with a sill in Puget Sound. The results show that tidally averaged mean outflow under the influence of such a constraint at the water surface could be reduced significantly. In the case of Hood Canal, preliminary results indicate that the presence of the floating bridgemight have increased the residence times in the basin by 8–13%, which could be an important factor affecting water quality.