The Canadian oil sands industry stores toxic oil sands process-affected water (OSPW) in large tailings ponds adjacent to the Athabasca River or its tributaries, raising concerns over potential seepage. Naphthenic acids (NAs; ...) are toxic components of OSPW, but are also natural components of bitumen and regional groundwaters, and may enter surface waters through anthropogenic or natural sources. This study used a selective high-resolution mass spectrometry method to examine total NA concentrations and NA profiles in OSPW (n = 2), Athabasca River pore water (n = 6, representing groundwater contributions) and surface waters (n = 58) from the Lower Athabasca Region. NA concentrations in surface water (< 2-80.8 ...g/L) were 100-fold lower than previously estimated. Principal components analysis (PCA) distinguished sample types based on NA profile, and correlations to water quality variables identified two sources of NAs: natural fatty acids, and bitumen-derived NAs. Analysis of NA data with water quality variables highlighted two tributaries to the Athabasca River -- Beaver River and McLean Creek -- as possibly receiving OSPW seepage. This study is the first comprehensive analysis of NA profiles in surface waters of the region, and demonstrates the need for highly selective analytical methods for source identification and in monitoring for potential effects of development on ambient water quality.