This paper evaluates the SIFOM-FVCOM system recently developed by the authors to simulate multiphysics coastal ocean flow phenomena, especially those at small scales. First, its formulation for buoyancy is examined with regard to solution accuracy and computational efficiency. Then, the system is used to track particles in circulations in the Jamaica Bay, demonstrating that large-scale patterns of trajectories of fluid particles are sensitive to small-scales flows from which they are released. Finally, a simulation is presented to illustrate the SIFOM-FVCOM system’s capability, which is beyond the reach of other existing models, to directly and simultaneously model large-scale storm surges as well as small-scale flow structures around bridge piers within the Hudson River during the Hurricane Sandy. This paper evaluates the SIFOM-FVCOM system recently developed by the authors to simulate multiphysics coastal ocean flow phenomena, especially those at small scales. First, its formulation for buoyancy is examined with regard to solution to accuracy and computational efficiency. Then, the system is used to track particles in circulations in the Jamaica Bay, demonstrating that large-scale patterns of trajectories of fluid particles are sensitive to small-scales flows from which they are released. Finally, a simulation is presented to illustrate the SIFOM-FVCOM system’s capability, which is beyond the reach of other existing models, to directly and simultaneously model large-scale storm surges as well as small-scale flow structures around bridge piers within the Hudson River during the Hurricane Sandy.