Selenium is an essential micro-nutrient for living organisms, but elevated concentrations of it in water can adversely affect health. Nitrate is often found in selenium-contaminated water and negatively correlates with selenium removal. In this study, we investigate the effect of nitrate co-existence on selenium bioremediation in chemically modified zeolite columns. Dynamic sorption-reduction experiments were conducted using natural and iron-coated zeolite columns to remove selenite and selenate oxyanions separately, with and without nitrate anions. Anaerobic sludge was included as microbial inoculum, while lactate was the sole electron donor. The initial selenium concentration (SeIV or SeVI) was 790 µg/L, the nitrate concentration was 620 mg/L, the pH was 7.5, and the flow rate was 3 mL/min. Before introducing nitrate ions, selenium reduction in all four columns reached approximately 99%. However, after introducing nitrate ions, selenate and selenite reduction efficiencies were reduced to approximately 93% and 60%, respectively. Biofilm microbial community composition, assessed by 16S rRNA sequencing, was distinct between the communities with and without nitrate anions. Specifically, in the absence of nitrate, biofilm communities are mainly composed of selenium-reducing bacteria (Veillonella, Bacteroides and Escherichia). In contrast, the presence of nitrate led to mostly denitrifying bacteria (Anaeromusa-Anaeroarcus, Lentimicrobium, Azospirillum and Endomicrobium). Further, comparison of diversity indices (Shannon index, Faith PD and Pielou’s) shows alteration in all indices in the presence of nitrate.