Freshwater mussels are among the most endangered groups of organisms on earth. They are particularly sensitive to environmental threats such as climate change, because of their sedentary nature and limited ability to respond behaviourally, e.g. by dispersal. The freshwater mussel Westralunio carteri, which is endemic to south-western Australia, has undergone a 38% reduction in range in the last 50 years, and with global climatic models predicting an increasingly warmer and dryer climate in the region, reduced water flow presents a substantial extinction risk. We document two recent cases of mass mortality in populations of W. carteri, associated with drying rivers. In both cases, larger mussels were significantly overrepresented in the cohort of dead mussels, compared to the surviving population. We hypothesised that this was due to smaller mussels being either better at moving horizontally into deeper pools, or better at moving vertically into the substrate to escape drying. Experimental studies found that the amount of horizontal movement by mussels was not affected by size, but there was a significant inverse relationship between the depth of burrowing and mussel size. Furthermore, depth of burrowing significantly reduced mortality rate in mussels exposed to drying conditions, although this relationship was lost when mussels were shaded. These findings have a number of implications: (1) predicted future reductions in water flow are likely to increase the mortality rate in W. carteri; (2) mortality risk will be greater for larger, older, more fecund mussels, producing a disproportionate decrease in recruitment; (3) any factors which affect burrowing ability will have a synergistic effect on mortality rate; (4) the adverse effects of drying rivers may be at least partially averted by increasing riparian shading.