Flow separation plays a key role in the development of dunes, and modeling the complicated flow behavior inside the flow separation zone requires much computational effort. To make a first step toward modeling dune development at reasonable temporal and spatial scales, a parameterization of the shape of the flow separation zone over two-dimensional dunes is proposed herein, in order to avoid modeling the complex flow inside the flow separation zone. Flow separation behind dunes, with an angle-of-repose slip face, is characterized by a large circulating leeside eddy, where a separation streamline forms the upper boundary of the recirculating eddy. Experimental data of turbulent flow over two-dimensional subaqueous bed forms are used to parameterize this separation streamline. The bed forms have various heights and height to length ratios, and a wide range of flow conditions is analyzed. This paper shows that the shape of the flow separation zone can be approximated by a third-order polynomial as a function of the distance away from the flow separation point. The coefficients of the polynomial can be estimated, independent of flow conditions, on the basis of bed form shape at the flow separation point and a constant angle of the separation streamline at the flow reattachment point.