Wave forecasting in ocean and coastal waters commonly relies on spectral models based on the spectral action balance equation. These models assume that different wave components are statistically independent and as a consequence cannot resolve wave interference due to statistical correlation between crossing waves, as may be found in, for instance, a focal zone. This study proposes a statistical model for the evolution of wave fields over non-uniform currents and bathymetry that retains the information on the correlation between different wave components. To this end, the quasi-coherent model (Smit & Janssen, J. Phys. Oceanogr., vol. 43, 2013, pp. 1741–1758) is extended to allow for wave–current interactions. The outcome is a generalized action balance model that predicts the evolution of the wave statistics over variable media, while preserving the effect of wave interferences. Two classical examples of wave–current interaction are considered to demonstrate the statistical contribution of wave interferences: (1) swell field propagation over a jet-like current and (2) the interaction of swell waves with a vortex ring. In both examples cross-correlation terms lead to development of prominent interference structures, which significantly change the wave statistics. Comparison with results of the SWAN model demonstrates that retention of cross-correlation terms is essential for accurate prediction of wave statistics in shear-current-induced focal zones.