Headwater streams have large surface-to-volume ratios that favor retention and removal of nitrogen.  Since headwater streams are highly vulnerable to anthropogenic impacts associated with land use change, we chose a highly modified headwater stream, impacted by urban development, to examine how geomorphic complexity is related to nitrogen uptake.  A key element of the study is a detailed protocol for characterizing physical complexity in terms of the spatial distribution of habitat units with distinct combinations of geomorphic, substrate, and hydraulic attributes.  We performed nutrient injections, along with the detailed physical characterization, in two segments of a Colorado Front Range urban stream to examine associations between geomorphic complexity and nitrate uptake.  We found that physical habitat complexity in one segment is associated with both hydraulic and geomorphic heterogeneity, while the other segment is geomorphically homogeneous but hydraulically complex.  Nitrate data collected from the nutrient injections in both segments were highly variable.  Further investigations, including spatially dense sampling of a conservative tracer, were performed to explore mixing and other sources of within-segment variability in nitrate uptake.