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Abstract Logjams in a stream create backwater conditions and locally force water to flow through the streambed, creating zones of transient storage within the surface and subsurface of a stream. We investigate the relative importance of logjam distribution density, logjam permeability, and discharge on transient storage in a simplified experimental channel. We use physical flume experiments in which we inject a salt tracer, monitor fluid conductivity breakthrough curves in surface water, and determine breakthrough‐curve skewness to characterize transient storage. We then develop a companion numerical model in HydroGeoSphere to reveal flow paths through the subsurface (or hyporheic zone) that contribute to some of the longest transient‐storage timescales. In both the flume experiments and numerical simulations, we observe backwater formation and an increase in hyporheic exchange at logjams. Observed complexities in transient storage behavior depend largely on surface water flow in the backwater zone. As expected, multiple successive logjams provide more pervasive hyporheic exchange by distributing the head drop at each jam, leading to distributed but shallow flow paths. Decreasing the permeability of a logjam or increasing the discharge both facilitate greater surface water storage and volumetric rate of hyporheic exchange. Understanding how logjam characteristics affect solute transport through both the channel and hyporheic zone has important management implications for rivers in forested, or historically forested, environments. 

Abstract Log jams alter gradients in hydraulic head, increase the area available for hyporheic exchange by creating backwater areas, and lead to the formation of multiple channel branches and bars that drive additional exchange. Here, we numerically simulated stream‐groundwater interactions for two constructed flume systems—one without jams and one with a series of three jams—to quantify the effects of interacting jam structures and channel branches on hyporheic exchange at three stream flow rates. In simulations without jams, average hyporheic exchange rates ranged from 2.1 × 10⁻⁴to 2.9 × 10⁻⁴ m/s for various stream discharge scenarios, but with jams, exchange rates increased to a range of 1.3 × 10⁻³–3.5 × 10⁻³ m/s. Largely due to these increased hyporheic exchange rates, jams increased stream‐groundwater connectivity or decreased the turnover length that stream water travels before interacting with the hyporheic zone, by an order of magnitude, and drove long flow paths that connected multiple jams and channel threads. Decreased turnover lengths corresponded with greater reaction significance per km, a measure of the potential for the hyporheic zone to influence stream water chemistry. For low‐flow conditions, log jams increased reaction significance per km five‐fold, from 0.07 to 0.35. Jams with larger volumes led to longer hyporheic residence times and path lengths that exhibited multiple scales of exchange. Additionally, the longest flow paths connecting multiple jams occurred in the reach with multiple channel branches. These findings suggest that large gains in hydrologic connectivity can be achieved by promoting in‐stream wood accumulation and the natural formation of both jams and branching channels.