In this study the levels and distribution of some persistent toxic substances (PTS) were investigated in soils, superficial water, and snow along an altitudinal gradient in the Laja River Basin (South Central Chile). The principal objective was to establish the basin’s contamination status. The working hypothesis was that PTS levels and distribution in the basin are dependent on the degree of anthropogenic intervention. Fifteen PAHs, seven PCBs congeners, and three organochlorine pesticides were studied in superficial soil and water samples obtained along the altitudinal gradient and from a coastal reference station (Lleu–Lleu River). Soil samples were extracted using accelerated solvent extraction with acetone/cyclohexane (1:1) for PAHs and organochlorine compounds. Contaminants were extracted from water and snow samples by liquid–liquid extraction (LLE). PAH and organochlorine compound quantification was carried out by HPLC with fluorescence detection and GC–MS, respectively. PCBs in soils presented four different profiles in the altitudinal gradient, mainly determined by their chlorination degree; these profiles were not observed for the chlorinated pesticides. In general, the detected levels for the analyzed compounds were low for soils when compared with soil data from other remote areas of the world. Higher ∑PAHs levels in soils were found in the station located at 227 masl (4243 ng g −1 TOC), in a forestry area and near a timber industry, where detected levels were up to eight times higher than the other sampling sites. In general, PAH levels and distribution seems to be dependent on local conditions. No pesticides were detected in surface waters. However, congeners of PCBs were detected in almost all sampling stations with the highest levels being found in Laja Lake waters, where 1.1 ng/l were observed. This concentration is two times higher than values reported for polluted lakes in the Northern Hemisphere. The presence of organochlorine compound in snow sampled at the highest elevation point of the basin is indicative of the transport and atmospheric deposition phenomena of α-HCH, γ-HCH and PCB 52, with values being similar to the levels reported in Canadian snow samples. We conclude that environmental PTS substance levels are in general relatively low, although PAHs may be of concern in some areas of the basin.