The pervasive effects of urban systems on the timing, spatial distribution, and quality of OM inputs presents a challenge for understanding how respiration regimes will respond to future urban change. Ecosystem respiration in streams is fueled by organic matter (OM) sources that vary in 2) the timing of their input to drainage networks, 2) lags associated with physical storage and transport, and 3) availability and quality as respiratory fuel. In relatively unaltered catchments, models that account for these processes can use time series of ecosystem respiration and proxies of OM inputs to disentangle the contributions of core components of respiration regimes including 1) autotroph-derived OM 2) particulate inputs associated with terrestrial litterfall 3) flow-associated dissolved OM and 4) long-term OM pools. To account for ongoing and future changes in respiration regimes, models of respiration regimes must account for the diversity of pathways by which OM delivery can differ along urbanization gradients and among urban systems with different contexts and histories. These include reductions and alterations of watershed and riparian canopy extent and composition, increased quantity and OM characteristics of floodwaters, direct delivery of wastewater via diffuse inputs and point sources, and changes in the capacity of channels to store organic matter. A comparative approach that explicitly addresses direct and indirect changes in organic matter dynamics of core regime components can help disentangle the amplifying and coutervailing processes that shape respiration regime responses to urban change.