Hydrokinetic turbine deployment in inland water reticulation systems such as irrigation canals has potential for future renewable energy development. Although research and development analysing the hydrodynamic effects of these turbines in tidal applications has been carried out, inland canal system applications with spatial constraints leading to possible blockage and backwater effects resulting from turbine deployment have not been considered. Some attempts have been made to develop backwater models, but these were site-specific and performed under constant operational conditions. Therefore, the aim of this work was to develop a generic and simplified method for calculating the backwater effect of HK turbines in inland systems. An analytical backwater approximation based on assumptions of performance metrics and inflow conditions was tested using validated computational fluid dynamics (CFD) models. For detailed prediction of the turbine effect on the flow field, CFD models based on Reynolds-averaged Navier–Stokes equations with Reynolds stress closure models were employed. Additionally, a multiphase model was validated through experimental results to capture the water surface profile and backwater effect with reasonable accuracy. The developed analytical backwater model showed good correlation with the experimental results. The model’s energy-based approach provides a simplified tool that is easily incorporated into simple backwater approximations, while also allowing the inclusion of retaining structures as additional blockages. The model utilizes only the flow velocity and the thrust coefficient, providing a useful tool for first-order analysis of the backwater from the deployment of inland turbine systems.