These data were compiled to monitor native fishes (particularly humpback chub Gila cypha) in the Little Colorado River, in the Grand Canyon, AZ. Objective(s) of our study were to evaluate the timing of native fish migration and the abundance of migratory and resident fishes between the Colorado and Little Colorado Rivers in the Grand Canyon. These data represent encounter histories for fishes - including array detections and physical captures. These data were collected in the lower 13.56 river kilometers of the Little Colorado River in April and May of 2021 and 2022. These data were collected by U.S. Fish and Wildlife Service (physical captures) and U.S. Geological Survey (array detections). These data can be used to evaluate yearly or size-based differences in timing and abundance of spawning fishes. These data can also be used to evaluate partial migration.