To characterize energy resources and study of hydrodynamic effects induced by marine hydrokinetic devices in tidal channels, numerical models need to provide reliable representations of turbine arrays. In regions disconnected from the grid, near coastal protected areas and other relevant economic activities, there is a pressing need to evaluate the impacts of limited-size arrays. Here, we use the emblematic Chacao Channel in Southern Chile to understand the effects of bathymetry and array placement on energy extraction in strongly tidal channels. We implement in FVCOM a parameterization from a previously derived high-resolution model to represent a group of turbines in different locations. We first analyze the complexity of the bathymetry to define the appropriate grid size and obtain a correct representation of the interaction of turbines with the bed morphology. We simulate a base case to identify three suitable locations in the channel where we analyze the effects of the turbines: From simulations we compute the changes in the mean velocity, turbulent kinetic energy (TKE), and bed shear stress. The results show that baseline velocities and TKE are the main factors on the momentum extraction despite the bed complexity. However, in flatter bathymetries, changes on TKE and bottom shear are significantly larger compared to complex morphologies, since turbine arrays modify considerably the original flow conditions. Simulations also provide additional insights that are critical to evaluate the local impacts, showing the directionally-dependent flow resistance of tidal channels, in which the interactions with bathymetry change the downstream effects of turbine arrays in flood or ebb regimes.