Analytical results from internal hydraulic theory are presented for a horizontal channel connecting river- and sea-basin waters of slightly different densities. The maximal exchange of inviscid, two-layer flow is analysed for such a system, for the case of a non-rectangular channel. The internal hydraulic theory has been extended to include internal energy losses and related net barotropic flow components in the surface layer. The hydraulic model is tested using archival field measurements in the Pärnu River mouth, where stratified bi-directional flow, accompanied by variable sea-level conditions and river water discharges, was observed. The study demonstrates that internal hydraulic theory predicts satisfactorily the stratified bi-directional fluxes and density-interface depths observed in the river mouth. In this study the two-layer exchange problem is solved with two control points, but the theory can be applied quite generally to predict the layer depths of the river and marine waters in the estuarine interaction zone.