Tidal stream turbines are becoming an affordable option for harvesting sustainable energy in coastal areas. They can be retrofitted in barrages, providing an integral solution for flood protection and emission-free power generation, within environmental constraints. To optimize the turbine-barrage configuration with respect to these objectives, simulation tools are needed to predict the efficiency of the turbines as well as their impact on the adjacent tidal system. These tools should be based on an accurate representation of the underlying flow processes, which cover a wide range of spatial scales — from meters at the barrage and turbines to tenths of kilometers in the tidal basin. This article presents the development of such a tool by linking an analytical model for turbine fences in barrage gates to a regional flow model. The turbine model is validated with experimental data, and data from a thoroughly monitored tidal energy pilot project. Simulations reveal how clustering the turbines in small arrays can increase their efficiency, owing to array blockage effects, with only little effect on the tidal exchange. We also demonstrate the potential of using turbine fences to manipulate the tidal jet, issued from the barrage, with benefits for coastal — and wildlife protection in the basin. The presented research helps understanding how turbine fences in barrages can be configured with high energy yield and calculated impact to the environment.