Abstract Connectivity within river networks governs the transport and aggregation of fluxes such as water, sediment, and nutrients. Here we focus on dynamic connectivity (DC) $(DC)$, defined by the time‐evolving connectivity that emerges as fluxes propagate and mix through the network, characterized by minimal‐flow connectivity DCmin $left(D{C}{min }right)$ and maximal‐flow connectivity DCmax $left(D{C}{max }right)$. Using 100 natural basins across the United States, we disentangle the roles of network geometry (link‐lengths) and topology (branching structure) in controlling the times to achieve DCmin $D{C}{min }$ and DCmax $D{C}{max }$. We find that link‐lengths decrease with stream order, and this geometric hierarchy primarily controls the time to DCmin $D{C}{min }$, whereas the time to DCmax $D{C}{max }$ is mainly governed by network topology. Placed in a climatic context, our results show that humid basins, characterized by stronger link‐length hierarchy and enhanced side branching, exhibit slower flux aggregation. This study provides new insights into how climate influences channel network geometry and topology, thereby controlling basin‐scale flux aggregation rates.