This article provides a deep analysis of the water quality at the upper basin of the Bogota River (Colombia) between 2008 and 2017. The Water Quality Index has been the indicator employed to determine the ecological status of the river. This index was chosen in order to normalize the analysis, given that it is commonly used by the Institute of Hydrology, Meteorology and Environmental Studies, a government agency of the Ministry of Environment and Sustainable Development of Colombia, to determine the state of surface effluents. The results obtained were organized in a double-entry matrix in order to relate the variables of the sample period and the sampling station. The research revealed an insufficient quality of water, demonstrating that the high stretch of the Bogota River basin has, in general, regular or acceptable water quality, while only five stations showed an acceptable status. Surprisingly, the stations located close to the wastewater treatment plants of the municipalities of Choconta, Suesca, Gachancipa, and Tocancipa, as well as Rio Negro, have a poor water quality, discharging a high load of contaminants into the river. Although great efforts have been made by Colombian authorities to restore the critical state of the majority of their aquatic ecosystems, recent implementation of policies and instruments have not shown significant achievements yet. For this reason, this study aims to present a powerful decision-tool for the monitoring and evaluation of correction measures implemented on this river basin. The data used in this research were provided by the Regional Autonomous Corporation of Cundinamarca.