The Water Quality Index is the numerical value that qualifies in categories, the water quality of a surface stream, based on the measurements obtained for a set of physicochemical and microbiological parameters registered in a water quality monitoring network. This indicator allows knowing the physical-chemical and microbiological quality conditions of a body of water and identifies contamination problems at a certain point. In the present study, the water quality was studied in 43 stations located in the Bogota river, considering different methodologies for calculating quality indices such as NSF, Oregon, IDEAM, Prati, and diffuse logic to establish the differences, advantages, and disadvantages of each method. Similarly, a correlation analysis was carried out between the parameters, and the land uses in the basin. The results indicated that all the indices showed regular or poor water quality for more than 80% of the stations for the temporal window studied. However, the methodology used in Colombia (ICA water quality index, in Spanish) has eclipsing problems in most of the evaluation points since where the water quality qualifies as good, other indices such as the fuzzy logic show a degree of contamination by any of the parameters mainly manganese or total suspended solids.