Lake Chapala is a natural ecosystem of Mexico, declared Ramsar site, currently, is an area with importance in the agricultural sector, tourism, and important source of drinking water in the Metropolitan area of Guadalajara, considered as a thermo regulatory body. This study used tools such as Rhtest, as well as analyzing extreme climate indices using RClimdex. In addition, the relationship with the change in water surface of Lake Chapala was assessed through the NDWI index, using Landsat images, between 1985 and 2018. According to the obtained results, the signs of climatic variability are detected in the study region, which, directly affects the basin runoff and water levels in the lake, as well as, the factor of water overexploitation in the basin, so it is considered that the lake conditions mostly depend on the type of management that is given to the resource. Finally, the results will help the understanding of climate variability and its water resources influence of the Lerma Chapala basin, which will assist in future research.