Compound-specific carbon and hydrogen isotope analysis (CSCIA and CSHIA) has been increasingly used to study the source, transport, and bioremediation of organic contaminants such as petroleum hydrocarbons. In natural aquatic systems, dissolved contaminants represent the bioavailable fraction that generally is of the greatest toxicological significance. However, determining the isotopic ratios of waterborne hydrophobic contaminants in natural waters is very challenging because of their extremely low concentrations (often at sub-parts ber billion, or even lower). To acquire sufficient quantities of polycyclic aromatic hydrocarbons with 10 ng/L concentration for CSHIA, more than 1000 L of water must be extracted. Conventional liquid/liquid or solid-phase extraction is not suitable for such large volume extractions. We have developed a new approach that is capable of efficiently sampling sub-parts per billion level waterborne petroleum hydrocarbons for CSIA. We use semipermeable membrane devices (SPMDs) to accumulate hydrophobic contaminants from polluted waters and then recover the compounds in the laboratory for CSIA. In this study, we demonstrate, under a variety of experimental conditions (different concentrations, temperatures, and turbulence levels), that SPMD-associated processes do not induce C and H isotopic fractionations. The applicability of SPMD-CSIA technology to natural systems is further demonstrated by determining the delta13C and deltaD values of petroleum hydrocarbons present in the Pawtuxet River, RI. Our results show that the combined SPMD-CSIA is an effective tool to investigate the source and fate of hydrophobic contaminants in the aquatic environments.