With the aim of understanding the impact of air pollution on human health and ecosystems in the tropical Andes region (TAR), we aim to couple the Weather Research and Forecasting Model (WRF) with the chemical transport models (CTM) Long-Term Ozone Simulation and European Operational Smog (LOTOS–EUROS), at high and regional resolutions, with and without assimilation. The factors set for WRF, are based on the optimized estimates of climate and weather in cities and urban heat islands in the TAR region. It is well known in the weather research and forecasting field, that the uncertainty of non-linear models is a major issue, thus making a sensitivity analysis essential. Consequently, this paper seeks to quantify the performance of the WRF model in the presence of disturbances to the initial conditions (IC), for an arbitrary set of state-space variables (pressure and temperature), simulating a disruption in the inputs of the model. To this aim, we considered three distributions over the error term: a normal standard distribution, a normal distribution, and an exponential distribution. We analyze the sensitivity of the outputs of the WRF model by employing non-parametric and robust statistical techniques, such as kernel distribution estimates, rank tests, and bootstrap. The results show that the WRF model is sensitive in time, space, and vertical levels to changes in the IC. Finally, we demonstrate that the error distribution of the output differs from the error distribution induced over the input data, especially for Gaussian distributions.