Activities of heterotrophic bacteria in nonsteady-state biofilms were evaluated using a simplified biofilm model in which formation and exchange of soluble microbial products (SMP) by nitrifiers and heterotrophs were considered. The model was applied to experimental results for a trace-level substrate removal. The model predictions indicated that SMP from nitrifiers contributed to supporting heterotrophic growth and their substrate removal potential. The biological interactions were more significant in cases of low influent substrate COD concentrations and increased with higher influent ammonium concentration. The introduction of SMP kinetics into the model captured the key aspects of removal and formation of COD components in biofilms receiving low influent substrate concentrations, such as nitrification filters for drinking water treatment and wastewater reuse.