Oil sands process-affected water (OSPW) is a toxic and poorly biodegradable mixture of sand, silt, heavy metals, and organics. In this study, qualitative and quantitative comparisons of naphthenic acids (NAs) were done using ultraperformance liquid chromatography time-of-flight mass spectrometry (UPLC TOF-MS), Fourier transform ion cyclotron resonance (FT-ICR) MS, and ion mobility spectrometry (IMS). The unique combination of these analyses allowed for the determination and correlation of NAs, oxidized NAs, and heteroatom (sulfur or nitrogen) NAs. Despite its lower resolution, UPLC-TOF MS was shown to offer a comparable level of reliability and precision as the high resolution FT-ICR MS. Additionally, the impacts of ozonation (35 mg/L utilized ozone dose) and subsequent NAs degradation on OSPW toxicity were assessed via a collection of organisms and toxicity end points using Vibrio fischeri (nonspecific), specific fish macrophage antimicrobial responses, and fish olfactory responses. Fish macrophages exposed to ozonated OSPW for 1 week showed higher production of reactive oxygen and nitrogen intermediates; however, after 12 weeks the responses were reduced significantly. Fish olfactory tests suggested that OSPW interfered with their perception of odorants. Current results indicate that the quantification of NAs species, using novel analytical methods, can be combined with various toxicity methods to assess the efficiency of OSPW treatment processes.