Batch and continuous biofilm reactors (BBR and CBR) were operated to treat raw and ozone-treated oil sands process-affected water (OSPW). In raw OSPW, the BBR removed less (24% vs. 29%) chemical oxygen demand (COD) than did the CBR. The CBR removed 14% of the acid-extractable fraction (AEF) from raw OSPW and 51% from ozonated OSPW, whereas the BBR had lower AEF removal efficiencies of 6.2% and 37% for raw and ozonated OSPW, respectively. NAs with low molecular weight were preferentially degraded over those with high molecular weight, and classical NA degradation was more effective in the CBR than in the BBR. CBR operation with ozone-treated OSPW allowed a favorable growth of bacteria due to the high bioavailability of low molecular weight compounds. Scanning electron micrographs showed that distinct biofilm and extracellular polymeric substances (EPS) were formed under continuous flow conditions, and that the biofilm was thicker in the CBR than in the BBR. Microbial community analysis using denaturing gradient gel electrophoresis (DGGE) revealed more bands in BBR biomass samples; 23 strains were identified in the BBR compared to 21 in the CBR. The continuous flow mode removed organic compounds more favorably than the batch mode from raw and ozonated OSPW.