Easily available organic substrates (e.g., peanut, walnut and almond shells and luffa sponge) were evaluated as potential filter material for permeable biobarrier systems. Higher removal efficiencies and rate constants were observed for lower (20%) substrate (e.g., peanut, walnut and luffa sponge) percentages indicating to the importance of substrate percentage. Rate constants were higher for total inorganic nitrogen removal (≥0.137 mg N/L/d) than for nitrate removal (≥0.127 mg N/L/d) in the batch bioreactors promising the capability of microorganisms in consuming substrate released nitrogen compounds. Continuous flow biobarriers revealed greater removal efficiencies (<1 mg NO3−–N/L) and rate constants (≥2.38 mg NO3−–N/L/d) that were related to better microbial performance with increased substrate contact. Different dissolved oxygen levels observed for peanut shell (≤7.45 mg O2/L) and luffa sponge columns (<3 mg O2/L) were indicating to the existence of different mechanisms and microorganisms during simultaneous heterotrophic nitrification and aerobic or anoxic denitrification. Luffa sponge was found to be the best candidate as a biobarrier substrate for a longer timescale, although walnut and almond shells may be excellent materials both supporting the denitrification process and permeability of barrier system.