Naphthenic acids are comprised of a large collection of saturated aliphatic and alicyclic carboxylic acids found in hydrocarbon deposits (petroleum, oil sands bitumen, and crude oils). Naphthenic acids enter surface water systems primarily through effluent discharge, but also through groundwater mixing and erosion of riverbank oil deposits. Of the possible environmental receptors (i.e., air, soil, and water), the most significant is water. Ambient levels of naphthenic acids in northern Alberta rivers in the Athabasca Oil Sands are generally below 1 mg L−1. However, tailings pond waters may contain as high as 110 mg L−1. The complexity of natural naphthenic acids in petroleum deposits poses an analytical challenge as reflected by the several techniques reported for quantitation of naphthenic acids in the environment. Although naphthenic acids are known to be persistent biomarkers used in identification of oil source maturation, little is established regarding their relative degradation pathways in aquatic environments. Published research related to the potential for microbiological degradation and adsorption to typical Athabasca Oil Sands soils reveal that naphthenic acids are likely to persist in the water column and, with prolonged exposure, accumulate in sediments. However, other than a very general knowledge of environmental persistence, the occurrence and fate of naphthenic acids has been sparsely studied. This article brings together some of those environmental persistence results, as well as detailed information regarding the origin of naphthenic acids in tailings ponds, chemistry and toxicological considerations, current analytical methods for aquatic sampling, and areas of future remediation research.