The hydrodynamic circulation model CMS-Flow (formerly known as M2D) is a two-dimensional, finite-difference numerical approximation of the depth-integrated continuity and momentum equations. Cells are defined on a staggered, rectilinear grid and can have constant or variable side lengths. The momentum equations are solved in a time-stepping manner first, followed by solution of the continuity equation, in which the updated velocities calculated by the momentum equations are applied. Features of the model include robust flooding and drying, wave-stress forcing, wind-speed dependent (time-varying) wind-drag coefficient, variably-spaced bottom friction coefficient, efficient grid storage in memory, and the convenience, through control statements, of independently turning on or off the advective terms, mixing terms, nonlinear continuity terms, and flooding and drying calculations. Hydrodynamic forcing capabilities are: water level, tidal constituents, flow-rate, wave stresses, and wind.