This study introduces a new scheme to make both turbulence and flow resistance modeling a dynamic function of tidal water depths and flow direction. The k−ε turbulence model is continuously adapted to local depth conditions and the Manning n bed roughness values are continuously made locally dependent on the direction of flow. Turbulence structure, production, and attenuation in estuaries are highly influenced by the fact that the flow occurs in ‘shallow water’. In hypertidal estuaries with complex bathymetries, the depths are highly variable in both time and space. In this paper, an adaptive correction scheme is introduced to dynamically adjust (in time and space) the k−ε turbulence model as a function of local flow depth. Furthermore, in the flow reversal portions of tidal rivers, flow direction changes cyclically during flood tides and ebb tides. This causes a direction-based pattern of bedforms that significantly affects the directional values of hydrodynamic bed resistance (Manning n). In this paper, an adaptive scheme accounts for flow directionality. The modifications are incorporated into a three-dimensional numerical hydrodynamic model (Delft3D). The resulting simulated water levels of the Koksoak hypertidal estuary are presented and are demonstratively in better agreement with observations than water levels simulated when not using the corrections. The results suggest that the proposed schemes can improve the accuracy of the turbulence and bed roughness models for simulations of shallow hypertidal estuarine flows with complex river bathymetries.