This work aims at determining the effect of wastewater input and hydrologic regimes on the epilithic algal colonization over artificial substrates in the Aburra–Medellin River. For this purpose, at eight stations in the river were installed 14 polypropylene baskets with 2000 grams of gravel as substrates in order to know the algae response to changes in water quality (reflected in changes in biological indices and also affected by fluctuations in water levels; i.e., flow rates, and therefore changes in its composition according to the hydrological cycle). Alterations generated in the composition and abundance of algae by wastewater discharges and change in water levels did not produce a pattern of colonization. Based on the above, it allowed to conclude that algae are sensitive organisms to particular events that affect water quality in the Aburra–Medellin River. KeywordsEpiphyton; Colonization; Algae; Water Quality of Aburra-Medellin River