The aquatic macro-invertebrate communities of 54 coffee farms in Cundinamarca and Santander were studied by comparing two agroforestry systems of Coffea arabica (with Rainforest Alliance-C and without certification-NC) in paired blocks with a completely randomized design in order to analyze the changes in abundance, composition and structure associated with water sources contamination. Physicochemical analyses and macro-invertebrate collections were carried out in the water springs of each farm during harvest and during non-harvest time in two points of the water body (start and end). In total, 11,275 samples were collected in both departments, distributed into 35 orders, 114 families and 352 morpho-species. There were significant differences in favor of the Certified farms with respect to the quality of the physical environment of ecosystems, evaluated with SVAP and CIPAV protocols in both departments. The BMWP biotic index indicated significant differences in favor of the Certified farms for both departments with average values of 118.4 ± 7.94 in C farms and 71.73 ± CE 7.6 in NC farms of Cundinamarca. For Santander, the BMWP values were 65 ± 7.14 and 48.8 ± 6.18 in NC farms. The physicochemical variables such as organic pollution load BOD and chemical demand of COD oxygen showed significant differences in favor of Certified farms. The conclusion is that with a Sustainable Agriculture adoption, there are better physical conditions and better water quality to support a more diverse population of aquatic macro-invertebrates.