ABSTRACT The Otún River watershed, located in the Colombian coffee region, provides water to over 700,000 inhabitants of the Risaralda department. Onion (Allium fistulosum) has been cultivated in this area since 1960, and it currently represents an important economic contribution for local farmers who have assimilated the models of intensive agricultural production with the common use of chemical inputs. The aim of this research paper is to identify management practices, and their potential impact on water quality for human supply in the Otún River. Using surveys conducted among local producers, a general farmers group with primary education was identified, who were not members of any producer association (≤9.1). Improper agricultural practices were identified in farms, where up to 1449 L ha−1 of diluted agrochemical supplies are used. Up to 70 different products with a large variety of toxicological categories (from a slightly toxic products class (III) to extremely toxic products (Ia)), for the management of pests and diseases of onion crops. With the Pesticide Impact Rating Index (PIRI) tool, a high impact of pesticide mobility toward water sources and risk to the ecosystem and humans was identified. In the water sources sampled, ten organochlorine pesticides and 16 organophosphate pesticides were detected.