Caño Barro is a secondary tributary of the Ayapel wetland complex (Ramsar site), Córdoba, Colombia. Despite its role connecting the Cauca River to the wetland, no previous study has assessed its environmental condition. This work presents an integrated geo-environmental evaluation combining morphometric analysis, in-situ water quality measurements, and total mercury (Hg-T) analysis across ten stations. The watershed (632.78 km2, Kc = 2.09) has a very low channel slope (0.017%), limiting sediment transport. Dissolved oxygen fell below 4.0 mg/L at three stations (P1 = 3.55, P3 = 2.58, P6 = 3.27 mg/L), indicating localized oxygen depletion. Hg-T exceeded the US EPA chronic criterion (CCC = 0.77 µg/L) at six of seven quantifiable stations (range: 0.54–2.01 µg/L), with one outlier of 97.46 µg/L requiring confirmation. The Conesa impact assessment classified mercury ecotoxicity as severe (I = −66), ranking it as the highest management priority. Conservation proposals include riparian restoration, erosion control, and mercury monitoring. These results provide the first environmental baseline for this Ramsar tributary and underscore the impacts of illegal gold mining on protected wetland systems.