The fate of pollutants in a biofilter is poorly understood. Quantifying the fate of carbon in the pollutant provides a better understanding of operation and improves modeling of biofilter performance. This study investigated the fate of carbon as influenced by temperature, water tension and pollutant concentrations. Soil biofilters degrading toluene were operated with no supplemental nutrient addition. Rigorous control of inlet concentration, temperature and water content was maintained with a differential biofilter. Temperature experiments were conducted at 20ᵒC, 30ᵒC and 40ᵒC and water tension was varied between 10 cmH2O and 20 cmH2O. The carbon recovery as CO2 ranged from 45% to 60% at a tension of 10 cmH2O and an inlet concentration of 170 ± 6 ppm with variable fractions of carbon ending up in the liquid and solid phases as determined by TOC. Further experiments maintaining the temperature at 40ᵒC and varying the tension to 20 cmH2O were done. Fractions of carbon recovered as CO2 significantly lowered to 32 % at a tension of 20 cmH2O. A third parameter was investigated at 30ᵒC by implementing a lower inlet toluene concentration of 96 ± 4 ppm and 10 cmH2O. The fraction of carbon recovered as CO2 was 72% illustrating significant variation in the carbon recovery with different environmental parameters. The endogenous respiration of C-CO2 from the soil bed was corrected for in the net CO2 produced. This result shows the dynamic variability of the various endpoints and product ratios on system inputs.