Aquatic vertebrates display a variety of control surfaces that are used for propulsion, stabilization, trim and maneuvering. Control surfaces include paired and median fins in fishes, and flippers and flukes in secondarily aquatic tetrapods. These structures initially evolved from embryonic fin folds in fishes and have been modified into complex control surfaces in derived aquatic tetrapods. Control surfaces function both actively and passively to produce torque about the center of mass by the generation of either lift or drag, or both, and thus produce vector forces to effect rectilinear locomotion, trim control and maneuvers. In addition to fins and flippers, there are other structures that act as control surfaces and enhance functionality. The entire body can act as a control surface and generate lift for stability in destabilizing flow regimes. Furthermore, control surfaces can undergo active shape change to enhance their performance, and a number of features act as secondary control structures: leading edge tubercles, wing-like canards, multiple fins in series, finlets, keels and trailing edge structures. These modifications to control surface design can alter flow to increase lift, reduce drag and enhance thrust in the case of propulsive fin-based systems in fishes and marine mammals, and are particularly interesting subjects for future research and application to engineered systems. Here, we review how modifications to control surfaces can alter flow and increase hydrodynamic performance.