This study aims to provide a thorough characterization of dissolved organics in oil sands process water (OSPW) in field-based aquatic mesocosms at both molecular and bulk measurement levels using multiple analytical methods. In a 3-year outdoor mesocosm experiment, the analysis of naphthenic acid (NA) species was conducted using ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOFMS). The results revealed the removal of both total NAs (38% and 35%) and classical NAs (O2–NAs, 58% and 49%) in undiluted and half-diluted OSPW, respectively. The increased ratios of oxidized NAs (O3–O6 NAs) to classical NAs suggested a transformation trend. The results also indicated that O2–NAs with higher carbon number and lower double bond equivalent (DBE) were more easily degraded in the mesocosm systems. Biomimetic extraction using solid-phase microextraction (BE-SPME) measurement displayed 26% (undiluted OSPW) and 30% (half-diluted OSPW) decrease in total bioavailable organics over 3 years. Naphthenic acids fraction compounds (NAFCs) obtained by liquid-liquid extraction (LLE) were also determined using Fourier transform infrared spectroscopy (FTIR). Reduction in acute toxicity for undiluted (43%) and half-diluted (26%) OSPW was observed over 3 years, which are well correlated with the decreases of NAs and BE-SPME concentrations. Moreover, BE-SPME values were found to be linearly correlated with total NAs concentrations (r = 0.96) and NAFCs (r = 0.96). Additionally, the linear relationships of individual O2–O6 NA species and BE-SPME concentrations unveiled the changes in the relative abundances of O2–O6 NA species in total bioavailable organics over time in the mesocosms. The present study has provided comprehensive insights by integrating various analytical methods, contributing valuable information for assessing the effectiveness of aquatic mesocosm systems in studying the temporal changes of organics in OSPW.