Many Best Management Practices (BMPs) have been developed to reduce excessive nutrients in stormwater runoff and mitigate harmful algal blooms in downstream receiving water bodies. This study demonstrates a new BMP by comparing two green sorption media (i.e., specialty adsorbents) for nutrient removal in cascade upflow biofiltration systems operated in parallel. The proposed filtration technology can control hydraulic gradients, prevent clogging and settlements, and increase hydraulic loading while removing more nutrients in an integrated physicochemical and microbiological treatment process. The two green sorption media being tested in this study include zero-valent-iron and perlite-based green sorption media (ZIPGEM) and biochar, iron, and perlite-integrated green sorption media (BIPGEM). BIPGEM or ZIPGEM was installed in two identical upflow bioreactors operated in sequence within each biofiltration system compared mainly for nitrate removal at three influent conditions for process reliability assessment. In addition, kinetics studies were conducted and analyzed to improve the understanding of reactor design. Dissolved organic nitrogen was monitored by using FT-ICR MS (Fourier transform ion cyclotron resonance mass spectrometer) whereas population dynamics of nitrifiers and denitrifiers were quantified by using RT-PCR (real time polymerase chain reaction). The process reliability was compared and confirmed based on the nitrate removal efficiencies, microbial population, and oxidation-reduction potential variations across the two biofiltration systems with different green sorption media. Results indicated that ZIPGEM performed slightly better than BIPGEM and the two identical upflow bioreactors operated in sequence within each biofiltration system exhibited steady operation with higher hydraulic loading relative to the downflow settings in the literature.