The hydrokinetic energy conversion system uses, in one embodiment, a perpendicular turbine coupled to an electrical generator and a laminar water flow shroud. The ballast and buoyancy system includes hydrofoils defining lateral sides of the shroud mounted on upper and lower decks. Ballast chambers are defined in some or all of the foils and each has a gas intake port and a water ballast output port. The shroud carries a source of compressed air, valves for control of air flow into the ballast chambers. The ballast and buoyancy system includes a control system with sensors for depth, pitch, yaw and roll of the shroud which generates valve control commands. Another embodiment utilizes an inline turbine and a radial water flow shroud with a plurality of circumferential hydrofoils. Struts mount the turbine near the primary hydrofoil and braces attach ring hydrofoils together. Alternatively, ballast chambers are defined in outboard-mounted ballast pods.