The oil industry is a major source of contamination in Peru, and wastewater and sediments containing oil include harmful substances that may have acute and chronic effects. This study determined polycyclic aromatic hydrocarbon (PAH) concentrations by GC/MS, mutagenicity using TA98 and TA100 bacterial strains with and without metabolic activation in the Muta-ChromoPlate™ test, and Microtox® 5-min EC50 values of Peruvian crude oil, and water and sediment pore water from the vicinity of San José de Saramuro on the Marañón River and Villa Trompeteros on the Corrientes River in Loreto, Peru. The highest total PAH concentration in both areas was found in water (Saramuro = 210.15 μg/ml, Trompeteros = 204.66 μg/ml). Total PAH concentrations in water from San José de Saramuro ranged from 9.90 to 210.15 μg/ml (mean = 66.48 μg/ml), while sediment pore water concentrations ranged from 2.19 to 70.41 μg/ml (mean = 24.33 μg/ml). All water samples tested from Saramuro and Trompeteros sites, and one out of four sediment pore water samples from Trompeteros, were found to be mutagenic (P < 0.001). One sediment pore water sample in Saramuro was determined to have a measurable toxicity (Microtox EC50 = 335.1 mg/l), and in Trompeteros, the EC50 in water and sediment pore water ranged from 25.67 to 133.86 mg/l. Peruvian crude oil was mutagenic using the TA98 strain with metabolic activation, and the EC50 was 17.18 mg/l. The two areas sampled had very high PAH concentrations that were most likely associated with oil activities, but did not lead to acute toxic effects. However, since most of the samples were mutagenic, it is thought that there is a greater potential for chronic effects.