This paper presents the development of a methodology for the simultaneous analysis of pentachlorophenol and hexachlorobenzene in natural waters affected by industrial residues, as its principal goal. Samples were collected in Quarentenário, São Vicente city, where most of the population utilize wells for their supply. The liquid-liquid extraction employed to remove PCP and HCB from the matrix for further identification and quantification, showed very good recovery and repeatability. The recovery range was between 81.5% and 103.0%, with a relative standard deviation of 2.4% and 4.1% for a fortification level of 10 ng L^-1. In addition, organochlorine compounds were determined by GC-ECD and/or GC-MS. The limit of quantification was 5 ng L^-1 for PCP and 2 ng L^-1 for HCB, which are below the maximum level allowed by the EC directives for pesticide residues in drinking water.