A control system for a continuous flow rotary blood pump is provided. A normal operating range of the blood pump is established. The normal operating range may comprise a normal pump flow range and a normal pressure head range. A target rotational speed of the pump is set in accordance with the normal operating range. A current operating condition of the blood pump is determined. The current operating condition may comprise a current pump flow, a current pressure head, and a current rotational speed of the pump. The current operating condition is compared with the normal operating range. An appropriate control algorithm is selected from a plurality of available control algorithms based on the comparison. The target rotational speed of the pump is adjusted using the selected control algorithm to maintain or recover the normal operating range.