An aerated submerged biofilm (ASBF) pilot plant has been developed. The present study optimized an inexpensive method of enhanced wastewater treatment. Over a period of three and one half months, a total of 11 batch runs were performed. By the fourth run, the biofilm had matured to the point that it consumed all the ammonia in 40 hours. The investigation aimed to present mathematical models for describing the dynamic behaviors of the dissolved organic matter removal and nitrification in the Aerated Submerged Biofilm (ASBF) for a batch reactor. Based on the experimental data from the batch system of the ASBF pilot plant, mathematical models were developed to predict dissolved organic matter and ammonia nitrogen removal rates as a function of heterotrophic and autotrophic bacteria populations, dissolved organic matter concentrations, ammonia nitrogen concentrations, dissolved oxygen concentrations, and temperature. The mathematical models for dissolved organic matter and ammonia nitrogen removal in ASBF include two differential equations reflecting heterotrophic and autotrophic bacteria populations, and a number of kinetic parameters. Consequently, the results provide a better insight into the dynamic behaviors of heterotrophic and autotrophic biofilm growth and their practical application to wastewater for dissolved organic matter and ammonia nitrogen removal process.