The extensive use of fertilizers in agriculture has led to widespread eutrophication. In this thesis, I explored sulfur-based autotrophic denitrification in agricultural headwater streams as means to remove nitrogen before it impacts receiving waters. I studied a stream mesocosm, simulating a headwater drainage ditch, amended with elemental sulfur. Nitrate removal efficiencies were as high as 99%, corresponding to effluent concentrations below 1 mg/L NO3--N. However, nitrate removals decreased over time, concurrent with accumulation of biomass on the bed surface, probably phototrophic growth. A model was developed to describe the hydraulic and biological reactions taking place within the mesocosm. The model captured trends in bulk liquid nitrate concentrations, but provided reasonable accuracy only when a high diffusive exchange coefficient was used. This suggests advective exchange with the bulk may be significant. Microbial community analysis of the sulfur-oxidizing biofilm suggested significant bacterial diversity existed within the mesocosm, with little variation in depth.