Ponds and wetlands around the world face anthropogenic pressures that threaten key ecosystem processes such as nutrient and organic matter cycling. Wetlands in arid and semi-arid regions are particularly at risk from uncertainty of water availability and competing pressures for use. Such threats are most acute for non-perennial systems that rely on occasional surface water flows to maintain important ecological functions. This study investigates the decomposition of an endemic macrophyte Cycnogeton procerum (R.Br.) Buchenau as a key ecosystem process in a chain-of-ponds wetland system, located in the intermittently flowing Mulwaree River, New South Wales, Australia. The aims of this study were to identify spatial and temporal patterns and the relative importance of microbial activity in macrophyte decomposition to improve our understanding of ecological processes in these intermittent systems. Exponential decomposition rates (proportional mass loss (g)) were highest during spring and summer (0.07-0.10 kd-1) and slower during autumn and winter (0.03-0.04 kd-1), reflecting seasonal drivers. Decomposition was significantly different in 9 mm and 150 μm mesh bags only during spring, suggesting decomposition was mostly performed by microbes, with invertebrate herbivores possibly only a factor during spring lotic conditions. Mesotrophic conditions, regulated by flow and internal macrophyte and algal dynamics appear to maintain a highly productive, macrophyte-dominated aquatic wetland system. Temperature was a major factor in decomposition rates and expected increases due to climate change will accentuate pressure on the resilience of the macrophyte community. Alterations caused by changing climate and anthropogenic land use place the ponds at high risk.