Dynamic water exchange between stream channels and hyporheic zones plays a crucial role in ecosystem processing and function. Key components of this influence can be derived via conservative breakthrough curve modeling, using foundational mathematical relationships between the water age distribution of hyporheic discharge, the rate of hyporheic exchange, and the hyporheic storage volume. We assess how alternative model assumptions affect estimates of hyporheic properties with real and simulated breakthrough curves. We employ a Bayesian curve fitting framework with a flexible, user-defined functional form for hyporheic water age distributions. Incorporating the hyporheic water age distribution perspective resulted in more accurately modeled tracer dynamics, while avoiding simplifying assumptions inherent to common models (e.g., well-mixed hyporheic zones, infinite maximum water residence times). Our approach similarly reveals that alternative models can yield vastly different outcomes for metrics of channel and hyporheic hydrology, with major implications for modeling biogeochemical processes.