Abstract – Synoptic fish surveys of river and irrigation canal sites and a path-analytic approach evaluate seasonal changes in fish assemblages in canal systems and river reaches of the middle Rio Grande, NM (USA). The objective was to assess how fish assemblages within the Isleta Reach respond to irrigation season and off-season variations in water and fish contributions from upstream river channels (Albuquerque Reach) and from the Peralta irrigation system. Eighteen species of fish were found in the irrigation canals, 13 in the Isleta Reach and 15 in the Albuquerque Reach. The proportion of nonnative fishes was higher in canals (56%) than in the river (11%). Species rank abundances were used in path analyses of fish species compositions during the irrigation season and off-season. During the irrigation season, path coefficients indicated fish movements downstream from the Albuquerque Reach (0.55) to the Isleta Reach exceeded contributions by the conveyance-return (0.29) and drain-return (0.05) canals. However, as the river de-watered the return canals were important refuge habitats for native fishes. The 0.05 value represented a major decline relative to the path coefficient for the upstream Peralta drain canal (0.72). During the off-season path coefficients indicated fish movements of 0.47 downstream in the river and 0.59 in the conveyance-return canal but a negligible value for the drain-return canal (-0.06). Irrigation management could be modified to favour native fish ecology by controlling movement of nonnative predators in canal systems and in providing refuge habitats for native fish during periods when water demand exceeds the supply.