A study was conducted on the industrial area waters of Guayanilla Bay to determine the potential for microbial utilization of toxic compounds such as fluorene, naphthalene, phenanthrene, phenol and pentachlorophenol (PCP) as a sole carbon source. Utilization of toxic substrates was determined by using Biolog MT Microplates inoculated with environmental samples. Water quality variables such as pH, salinity, temperature and turbidity were also measured. In general, temporal changes in the Bay influenced the utilization of these compounds, with increased utilization of toxic compounds during rainy season. Heavy rainfall caused perturbation of sediments rich in organic matter, as was evidenced by increased turbidities. This provided both the environment and the substrates necessary for enhanced microbial growth and activity. The levels of dissolved oxygen in the bay water decreased as a result of increased biological activity. Other environmental factors such as fluctuations in temperature, salinity, and pH appear to have little or no impact on microbial utilization of toxic compounds in the bay water.