The diel variation in boat electrofishing catches was investigated on the lower Murray River (south-eastern Australia), downstream of three low-level weirs. Fish assemblage composition did not differ among three sites, but differed substantially between day and night. Significantly more small-bodied species (e.g. Australian smelt Retropinna semoni, flyspecked hardyhead Craterocephalus stercusmuscarum, bony herring Nematalosa erebi and Murray rainbowfish Melanotaenia fluviatilis) and some large-bodied predators (e.g. golden perch Macquaria ambigua) were caught during daytime samples. Significantly more flatheaded gudgeon Phylipnodon grandiceps, carp gudgeon Hypseleotris spp. and perch Perca fluviatilis were collected at night. The size composition of the fish assemblage also changed over the diel cycle. Significantly smaller goldfish Carassius auratus, flyspecked hardyhead, bony herring and Australian smelt were sampled during the day, while generally smaller individuals of golden perch and the common carp Cyprinus carpio were caught at night. These findings suggest that sampling during both day and night is required to adequately characterize riverine fish assemblages in the context of fish migration studies.