Seasonal dynamics of water circulation and exchange flows in a shallow lagoon-inlet-coastal ocean system

•3D hydrodynamic model is applied to a lagoonal system at a seasonal timescale.•Seasonal circulation in the surface is stronger than that in the bottom layer.•Seasonal dynamic is controlled by tide, affected by wind, wave, density, and inlet.•Wind direction is key to the seasonal dynamics in the lagoon.•Tides are important to water circulation and exchange flows in the upper bay. A wave–current coupled, unstructured-grid, three-dimensional hydrodynamic model was applied to investigate the seasonal dynamics of the Maryland Coastal Bays system. The model's performance was validated successfully against hydrodynamic observations from the spring to fall of 2014, and the driving forces of water circulation and exchange flows were discussed. Results indicate that seasonal dynamics are primarily controlled by tides, modulated by winds, waves, and density variations, and regulated by the inlet orientation and geometry. Seasonal circulation in the surface layer is stronger than that near the bottom. The strong coastal circulation, net outflows via inlets, and the clockwise movements in the southern Isle of Wight Bay are primarily controlled by tides. The directional alignment between winds and the bay's principal axis and inlet orientation are key to the seasonal circulation and exchange flows in Sinepuxent Bay and via inlets. Wave-induced effects are comparable to tides in particular regions (e.g., reaching 30 cm/s in Isle of Wight Bay), and much larger than those caused by density variations overall. Additional numerical experiments indicate that spatial variations in salinity are mainly responsible for the density-induced circulation (e.g., 6 cm/s at the mouth of Newport River in Newport Bay). Further analysis indicates that the net exchange flows vary from the surface to bottom layers (e.g., different magnitudes or transporting directions) both in the lagoon and via the paired inlets. This work is beneficial to coastal communities and numerical modelers in understanding the dynamics of shallow lagoon-inlet-coastal ocean systems at a seasonal timescale.