AbstractDissolved oxygen (DO) is critical for aquatic ecosystems, however, few studies have focused on the long‐term DO dynamics in hyporheic zones, which are a function of both transport (hydrologic exchange between river and hyporheic zone) and uptake by biogeochemical reactions or respiration. We explore the dynamics of temperature and DO at 10, 20, and 35 cm depth beneath the East River, Colorado, from July–October 2017 (relatively normal water year) and April to October 2018 (comparatively low flow year), enabled by distinctive, in‐situ, high frequency (Δt = 5 min) sensors that provided continuous time‐series from the undisturbed study site over 14 months. We expect that hyporheic DO, which has a regular daily fluctuation pattern, is supplied by the surface water (at all times we estimate downwelling) and that diurnal hyporheic DO temporal patterns should be aligned with diurnal hyporheic temperature patterns. However, this was not found to be the case. Hyporheic DO becomes depleted briefly at 20 and 35 cm depths in 2017, and at all three hyporheic depths for extended periods in 2018. Whereas diurnal temperature fluctuations have consistent timings of maxima and minima, hyporheic DO rarely has as regular a pattern, and daily ranges are inconsistent. Rainfall events caused some of these changes to diurnal hyporheic DO patterns without repeatable effects. Antecedent snowpack conditions influence streamflow dynamics and therefore hyporheic DO dynamics in this alpine river. These results also point to the strong and variable influence of hyporheic microbial communities regulating hyporheic DO.