A control system controls a progressive cavity pump driven by a rod. The rod is powered by a prime mover, such as a variable speed drive. A proximity sensor outputs signals responsive to rotational positioning of the rod. A controller receives the signals and computes a time interval between selected signals corresponding to a selected number of rod rotations. The controller references a data set, compares the computed time interval with the data set, and selectively increases, decreases, or cycles power to the prime mover in response thereto, thereby controlling the fluid level within the well.