Migratory fishes often spawn across broad spatial scales to limit intraspecific interactions among mature and immature individuals, leading to long‐distance movements of both adults and offspring. Thus, offspring are potentially exposed to a range of environmental conditions throughout their development that affect growth, survival, and recruitment. Migratory suckers (family Catostomidae) can be used to test spatial variation in early life stage experiences for iteroparous fishes. We use the Flannelmouth Sucker Catostomus latipinnis, a fish that is endemic to the American Southwest, to illustrate how larval and juvenile stages are affected by the distance of upstream spawning migration in tributaries that vary in flow regime and habitat availability (i.e., perennial versus intermittent streams). Remote detection of PIT‐tagged migrating adults indicated that spawning and larval rearing sites were distributed over 32 km within McElmo Creek, a perennial tributary to the San Juan River, Utah. Physical sampling of an upstream intermittent tributary, the Mancos River, New Mexico showed that spawning adults—and then larvae—were restricted to within 1 km of the main‐stem river. Quantile regression demonstrated recruitment of larvae to the juvenile stage was significantly (i.e., up to 2 weeks) faster in more upstream reaches of the perennial tributary, potentially due to more constant thermal regimes. Spatial differences in animal community structure at sites with larval Flannelmouth Sucker indicated that the potential for predation and competition was greatest in upstream reaches. Small, rare, and even intermittent tributaries concentrate spawning activity that dictates larval sucker experiences. Conserving, maintaining, and enhancing connectivity via flows synchronized with spawning and rearing are critical steps to protect migratory suckers in arid environments.