Headwater streams are critical sites for nitrogen processing in lotic ecosystems but the identity and function of specific groups of microorganisms that drive these processes remain poorly understood.  Identification of which microbial groups and functions are present with varying supply of nutrients and organic matter will promote understanding of biological controls of nitrogen processing rates.  Here we report the relative abundance of ammonia monooxygenase (amoA) genes specific to Archaea, Beta- and Gamma-Proteobacteria in forested headwater streams with contrasting nutrient and organic matter content.  Sediment samples were collected at multiple time and sampling points from nutrient enriched (NE), organic matter removal (OMR), and control streams located at the Coweeta LTER (NC, USA).  Microbial abundance increased significantly with resource availability; microbes were most abundant in the NE stream followed by the control and OMR streams, respectively.  The ammonia oxidizing community shifted from a predominance of archaeal amoA genes in the OMR stream to a greater proportion of gamma- and beta-proteobacterial amoA genes in the NE stream, while relative abundances in the control stream were intermediate of the two treatments.  This suggests that ammonia oxidation is mediated primarily by archaea under more oligotrophic conditions, while beta- and gamma-proteobacteria predominate under higher resource conditions.