Excess nitrogen input from nonpoint sources driven by hydrologic and anthropogenic disturbances has become a significant ecological challenge in receiving water bodies. Moreover, nitrate removal by cost-effective filtration media has still not performed up to expectation because of the knowledge gap in the transitional phase from physicochemical to microbiological processes. This study developed three cost-effective, sustainable, and adaptable green sorption media (GSM), namely CPS (clay–perlite with sand sorption media), ZIPGEM (zero-valent iron and perlite green environmental media), and BIPGEM (biochar, zero-valent iron, and perlite-based green environmental media), made of readily available and recyclable materials, to compare nitrate removal methods for stormwater treatment and elucidate the transitional phase. The primary adsorption mechanism was chemisorption, and subsequent biofilm growth sustained removal efficiency for a long-lasting period. Adsorption kinetics, adsorption equilibrium, material characterization, and fixed-bed column experiments with a 2-stage cultivation approach were undertaken to characterize the transitional phase in these GSM, based on breakthrough curves, maximum adsorption capacity, and microbial population dynamics for nitrification and denitrification. As shown in the column study, BIPGEM had the highest adsorption capacity (7.637 mg∙g−1), followed by ZIPGEM (2.16 mg∙g−1), and CPS (0.1798mg∙g−1). The biochar in BIPGEM provides a better cultivation environment for nitrifying and denitrifying bacteria, contributing sufficient electron donors. Biofilm production and maturation enabled the BIPGEM to maintain 30% nitrate removal in a steady state even after 2,000hours of operation in the first stage. When the biofilm reached maturation, BIPGEM’s nitrate removal percentage was up to 70% via denitrification in the second stage.