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Flow regulation and fragmentation of the world's rivers threaten the integrity of freshwater ecosystems and have resulted in the loss or decline of numerous fish species. Pelagic-spawning fishes (pelagophils) are thought to be particularly susceptible to river regulation because their early life stages (ichthyoplankton) drift until becoming free-swimming, although the extent of transport is largely unknown. Transport velocity and distance were determined for passively drifting particles, which mimicked physical properties of ichthyoplankton, in two large, regulated rivers (Rio Grande and Pecos River) of the arid Southwest United States. Particle drift data were incorporated into celerity-discharge equations (r2 > 0.90; P < 0.001), and reach-specific transport velocity was modeled as a function of discharge. Transport velocities of particles exceeded 0.7 m/s in all river reaches during typical spawning flows (i.e., reservoir releases or rainstorms) and were greatest in highly incised and narrow channel reaches. Mean transport distance of particles released in the Pecos River during sustained reservoir flows (141.1 km; 95% CI = 117.0-177.5 km) was significantly longer than during declining reservoir flows that mimicked a natural rainstorm (52.4 km; 95% CI = 48.8-56.5 km). Mean transport distance of particles in the Rio Grande during sustained reservoir flows was 138.7 km (95% CI = 131.0-147.2 km). There are 68 dams and 13 reservoirs that fragment habitats and regulate flow in the Rio Grande Basin (Rio Grande and Pecos River) in areas historically occupied by pelagophils. While the basin historically provided 4029 km of free-flowing riverine habitat, reservoir habitat now represents > 10% of the longitudinal distance. Only five unfragmented nonreservoir reaches > 100 km remain in the Rio Grande, and two remain in the Pecos River. Pelagophils were extirpated from all reservoirs and from nearly all short, fragmented reaches (< 100 km) of the Rio Grande Basin, but at least some fraction persisted in all longer reaches (> 100 km). The recovery and long-term persistence of pelagophils in regulated rivers, including those in this study, will likely depend on reestablishment and protection of long unfragmented reaches coupled with mimicry of the natural flow regime.