Studies in the Northern Hemisphere have shown that mussels play important roles as benthic-pelagic couplers in freshwater systems, transferring filtered material, nutrients, and energy from the water column to sediments, through biodeposition and excretion. However, we know little of the functional roles of species of the Southern Hemisphere Hyriidae, the second most diverse family of the Unionoida. The aims of this study were to determine the biodeposition and excretion rates of nutrients and organic matter of the hyriid Alathyria jacksoni in an unregulated Australian river and test experimentally if the physical structure and biodeposition of A. jacksoni influenced sediment nutrients, organic matter, periphyton concentrations and meiofauna densities. In a lowland Australian river in late summer over 4 weeks, we measured biodeposition and excretion rates of A. jacksoni, and conducted a mesocosm experiment, during which we compared the effects of live mussels, dead mussel shells (shams), and controls without mussels on nutrients, organic matter, and meiofauna invertebrate densities in the sediment. Mean (± SE) mass of biodeposition was 70.85 ± 3.20 mg mussel−1 hr−1 and the relative rates of inorganic and organic biodeposition were 60.9 ± 3.1 and 9.9 ± 0.8 mg mussel−1 hr−1, respectively. Organic matter was significantly greater in the sediment of the mesocosms with live mussels than in that of the control mesocosms. There was also a trend of greater mean sediment chlorophyll-a and total nitrogen concentrations in mussel treatments than in the controls. No significant difference was detected in sediment total phosphorous between mussel and control enclosures. The valves of live mussels had significantly higher amounts of organic material and chlorophyll-a concentrations than the valves of sham mussels. There was a consistent trend of higher meiofauna densities collected in the benthos of the mussel enclosures than the control enclosures for total density and densities of Rotifera, Copepoda, Cladocera, Diptera, Oligocheata, Nematoda, and Ostracoda; this trend was near significant for total density; and significant for densities of Ostracoda, Rotifera, Cladocera, and Nematoda. Using our biodeposition and excretion rate estimates, and estimates of population size of A. jacksoni in the Lower Ovens River, we estimated that in a typical 1-km reach in a month over summer, A. jacksoni would be biodepositing approximately 4.8 kg/day of organic matter (dry mass), 137 g N/day and 19 g P/day, and excreting 21 g N/day and 3.7 g P/day. Our findings are similar to those for Northern Hemisphere families of the Unionoida and serve to highlight the roles mussels play in processing of organic matter and cycling of nutrients in freshwater ecosystems.