Dynamic water exchange between stream channels and hyporheic zones plays a crucial role in ecosystem processing and function, yet adequately representing these dynamics in whole-stream metabolism models remains challenging. We demonstrate an approach for explicitly incorporating hyporheic hydrology into ecosystem process models by testing how foundational mathematical relationships between residence time, hyporheic exchange, and subsurface storage affect metabolite delivery and thus influence estimates of ecosystem metabolism. Our analysis employs a flexible, user-defined functional form for hyporheic water age distributions, which avoids inappropriate assumptions inherent to simpler models, such as well-mixed hyporheic zones and/or infinite water residence times. This framework allows us to more realistically represent the dynamic nature of hyporheic zone effects on whole ecosystem metabolism and, critically, to distinguish between the effects of hydrologic delivery and biotic activity. We evaluate how this integrated approach affects our ability to estimate ecosystem metabolism parameters and discuss implications for modeling coupled hydrologic-biotic processes in real stream systems.