Urban development of watersheds increases runoff and nitrogen loads by adding urban impervious surfaces and increasing the hydrologic connectivity of these surfaces to streams. Storm water control measures (SCMs) are designed to disrupt this connectivity by retaining water in biologically active depressions where nitrogen retention, transformation, and removal occur. This work applies a mechanistic, spatially distributed, hydroecological model (RHESSys) to a suburban watershed in Charlotte, NC, with 15% total imperviousness (TI) and 33% watershed area mitigated by SCMs. We developed emergent relationships between watershed‐scale predictors (TI and connectivity to SCMs) and water and nitrogen response variables (storm water runoff ratios and nitrogen load by species). Results showed that annual runoff ratios were insensitive to increases in connectivity to SCMs (varying by ~1% of rainfall) because SCMs did not substantially increase evaporation but that runoff ratios increased by an average 0.2% per 1% increase in TI due to decreases in transpiration in the watershed. Generally, nitrate loads increased with TI but decreased as more surfaces were mitigated by SCMs. However, these nitrate reductions corresponded to increased export of dissolved organic nitrogen and ammonium. Together, these results indicate that SCMs act as both removers and transformers of nitrogen at the watershed scale. SCMs showed a net assimilation of nitrogen in warm months and net release in cool months, which offset the timing of nitrogen export relative to inputs. This work highlights that using a hydroecological, process‐based model reveals both the emergent relationships between watershed condition and response and the processes controlling those relationships.