The use of numerical weather prediction (NWP) model to dynamically downscale coarse climate reanalysis data allows for the capture of processes that are influenced by land cover and topographic features. Climate reanalysis downscaling is useful for hydrology modeling, where catchment processes happen on a spatial scale that is not represented in reanalysis models. Selecting proper parameterization in the NWP for downscaling is crucial to downscale the climate variables of interest. In this work, we are interested in identifying at least one combination of physics in the Weather Research Forecast (WRF) model that performs well in our area of study that covers the Baker River Basin and the Northern Patagonian Icecap (NPI) in the south of Chile. We used ERA-Interim reanalysis data to run WRF in twenty-four different combinations of physics for three years in a nested domain of 22.5 and 4.5 km with 34 vertical levels. From more to less confident, we found that, for the planetary boundary layer (PBL), the best option is to use YSU; for the land surface model (LSM), the best option is the five-Layer Thermal, RRTM for longwave, Dudhia for short wave radiation, and Thompson for the microphysics. In general, the model did well for temperature (average, minimum, maximum) for most of the observation points and configurations. Precipitation was good, but just a few configurations stood out (i.e., conf-9 and conf-10). Surface pressure and Relative Humidity results were not good or bad, and it depends on the statistics with which we evaluate the time series (i.e., KGE or NSE). The results for wind speed were inferior; there was a warm bias in all of the stations. Once we identify the best configuration in our experiment, we run WRF for one year using ERA5 and FNL0832 climate reanalysis. Our results indicate that Era-interim provided better results for precipitation. In the case of temperature, FNL0832 gave better results; however, all of the models’ performances were good. Therefore, working with ERA-Interim seems the best option in this region with the physics selected. We did not experiment with changes in resolution, which may have improved results with ERA5 that has a better spatial and temporal resolution.