Abstract Temporal changes in the population sizes of seven migratory species were assessed over a 2-year period prior to the construction of a fishway on the Murrumbidgee River, Australia. Mark-recapture (Chapman–Petersen) and Jackknife removal methods were used at 3-month intervals to determine the composition and sizes of migratory fish populations. No difference in population size estimate was detected between the two methods. However, the Jackknife removal estimator generally provided less variable estimates for a greater number of species. Population sizes were greatest during summer and autumn when bony herring, Nematalosa erebi Günther, and common carp, Cyprinus carpio L., dominated the migratory community. Both estimators provided data essential to further the development of an appropriate fish passage facility and could be applied to other sites where the size of migratory fish populations is of interest.