Freshwater mussels are riverine ecosystem engineers they modify substrates, mediate water quality, provide food and habitat for other organisms and play a significant role in the biogeochemical cycling of nutrients. They are also globally threatened. Three species occur in the northern Murray-Darling Basin (nMDB) rivers – the large ‘river mussels’ Alathyria jacksoni and Alathyria condola and the smaller ‘floodplain/billabong mussel’ Velesunio ambiguus. This study focussed on A. jacksoni and the impact of the 2017-2020 drought on survival and distribution. A boosted regression tree (BRT model) identified upstream catchment area, average catchment slope and average saturated hydraulic conductivity; all relating to runoff and water availability influenced the distribution throughout the nMDB; with A. jacksoni likely to occur across the mid to lowland reaches of the Barwon-Darling River and its associated north-eastern and eastern tributaries, but be absent from the westerly Warrego and Paroo Rivers. Hydrological analysis suggested that the duration of cease to flow (CTF) events in the hydrological drought of 2017-2020 were longer, and sometimes more than double the duration, of the maximum CTF length for the preceding 37 years, with the lower gauges on the tributary rivers and the gauges on the Barwon-Darling having the greatest difference. The field survey of 90 sites suggested evidence of A. jacksoni in reasonable abundance in all rivers except the Gwydir and Macintyre, however, throughout most of tributaries sampled in 2020 most individuals were deceased and at no site were only live mussels observed. The greatest abundance of A. jacksoni, both alive and dead, was observed in the lower Darling below Menindee; overall site mortality was estimated between 20-100% across the nMDB. The extensive drying of the Barwon-Darling system during the drought from 2017-2020 likely had a significant impact on mussel populations and particularly populations of the long-lived river mussel A. jacksoni.