We present an overview of quantitative microinvertebrate sampling in the main channel of the Lower Murray River (LMR) below Lock 6 (Renmark) and Lock 1 (Blanchetown). During spring–summer of 2014–2018, 700 4-l Haney trap samples collected >300 taxa of microinvertebrates, at densities to 3,000 ind. l-1 with up to 62 taxa in 1-ml aliquots. Hydrology varied during the monitoring period from relatively low, stable, in-channel flows during 2014–2016 to overbank floods in 2016–17, and a return to low flows in 2017-18. Considerably greater microinvertebrate diversity during 2016-17 sampling below both Locks, compared to other years, reflected disparate sources from above Lock 6, primarily Murray River, indicated by taxa known only from that catchment. Warm water taxa indicative of the Darling River (or by diversion, Lake Victoria) appeared in trap samples late December–January. The relatively high proportion of littoral, epiphytic and epibenthic taxa recorded in the main channel (to 70% of the ‘plankton’), particularly testate rhizopods and littoral rotifers, reflected floodplain returns following overbank flooding and weir pool recession. Introduced taxa first collected during 2015-16 were again recorded during 2016-17 and 2017-18. Novel taxa, including the tropical Brachionus durgae, (India), Keratella americana and Hexarthra braziliensis (America), and the Eurasian Daphnia galeata were recorded at both Locks. D. galeata is invasive in North America following introduction into the Great Lakes. Barcoding of the LMR population established a Northern Hemisphere origin, but not whether Eurasian or North American. Dominance of the river zooplankton September–November 2016 by the tintinnid ciliate Codonaria is unusual for freshwater/riverine systems. Elsewhere the genus is marine/estuarine. Throughout the study period the LMR zooplankton was dominated by protists/rotifers, with small seasonal pulses of microcrustaceans. The study demonstrates the influence of flow on spatio-temporal patterns of zooplankton assemblage in a large temperate lowland river, which could inform river management.