A Water Quality Index (WQI) is a formulation that enables the estimation of the overall quality of a water body based on significant parameters. One example of this is the well-known and widely accepted NSF-WQI, which is frequently used to assess chemical, physical, and microbiologic features of waterbodies in temperate latitudes. In this work, a well-structured method, completely based on multivariate statistical methods and historical data distributions, was used to develop an ecosystem specific water quality index (ES-WQI). Lake Cajititlán, a subtropical Mexican lake located in Tlajomulco de Zúñiga, was selected as a case of study because it is an endorheic shallow lake that shows signs of high levels of eutrophication due to anthropogenic contamination. As a result of the contamination, and its sensibility to changes in the water level, it undergoes important changes in its water features, such as turbidity and intense green color, and experiences massive events of fish mortality. The proposed ES-WQI describes the changes in water quality over the year well and correlates with the capability of the lake to support aquatic life, as the lowest estimated values coincide with the biggest events of massive fish mortality in the lake. Furthermore, the ES-WQI clearly differentiates between typical cyclic behaviors and actual deteriorating trends and is capable of tracking incremental changes all over the range of the possible concentration values of the water quality parameters.