In Colombia little attention has been paid to river pollution with Polycyclic Aromatic Hydrocarbons (PAHs). Low environmental control and legislation in such emerging region could significantly contribute to high PAHs releases. In this study, we report the presence of PAHs in water and sediments of the Cauca River (Colombia). Three sampling campaigns were carried out between May 2010 and June 2011, and the samples were collected at eight relevant sites. The sampling time included measuring before, during, and after a season of heavy rains, which were influenced by the global coupled ocean-atmospheric phenomenon, which affected tropical countries with huge flooding, commonly called "La Niña", and/or "El Niño" Southern Oscillation (ENSO). The highest mean ∑PAH concentrations were 4476.5 ng/l and 1582.7 ng/g in water and sediments, respectively. The PAHs most detected were Benzo[b]fluoranthene, Benzo[k]fluoranthene, and Pyrene in sediments; and Fluorene, Acenaphtylene, and Anthracene in water. After the season of rains statistically significant higher PAH concentrations were detected. The results of the study were compared to other rivers worldwide at both environmental compartments, and did not show concentrations of special concern. In some sites, concentrations detected of PAHs were higher than screening benchmarks for ecological protection. Estimation of human health risks was carried out, and the results suggested some likely carcinogenic effects due to PAHs especially in children exposed during current recreational swimming and adults working in low technology sand extraction.