Fish habitats and reproduction can be significantly altered downstream of hydroelectric power plants operated by hydropeaking and resulting in rapid and frequent changes in river hydrodynamic conditions. To mitigate the impacts, it is necessary to maintain the habitat quality through operational measures. The microhabitat method, coupling 1 D or 2 D hydraulic simulations to biological models, is a useful tool to assess the evolution of hydromorphological parameters and fish habitats and define these mitigation measures. Calibration of the hydraulic model must be carried out carefully because the model must accurately reproduce hydraulic conditions from low to high flows. The objective is therefore to evaluate the sensitivity of the habitat value as a function of the type of calibration and the friction law for shallow habitats. The analysis is performed by estimating the uncertainty in fish habitat values resulting from Strickler’s law or Nikuradse’s law. The study is carried out on a river in the French Pyrenees based on the modeling of 2 stations with different cross-sectional shapes, one with progressive overflow and the other without these phenomena. Thanks to field measurements at low and high flowrates, the calibration process showed that the friction coefficient can be multiplied by 2. Two dimensionnal simulations give similar results to those obtained with 1 D when the flow remains unidirectional but differ for areas with high overflows. Calibration and models can lead to different conclusions regarding the estimation of habitat modifications due to hydropeaking operation and the definition of base flow and maximum turbine discharge.