Ecosystem metabolism is a key process that is tied to trophic dynamics and biogeochemical cycles which include the formation and utilization of organic matter (DeAngelis, 2012). Planktonic metabolism is regarded as the balance between gross primary productivity of phytoplankton (GPP) and planktonic respiration (PR) (Hoellein et al., 2013). Together, planktonic and benthic metabolism comprise aquatic metabolism. The balance between GPP and PR determines whether an aquatic ecosystem is autotrophic, producing more carbon, or heterotrophic, consuming more carbon (Wetzel & Likens, 1991). Planktonic metabolism varies temporally as well as spatially (Caffrey, 2004), and is affected by various environmental factors including hydrology, geomorphology, light, temperature, nutrient availability and microbial communities (Belnap et al., 2005). Understanding the relationships between these factors is essential for developing effective management plans for wetlands (Bunn et al., 2006).Water allocations for the environment ("environmental flows") are an important part of the hydrology of many semi-arid rivers and floodplain wetlands, including the wetlands of national and international importance located in the 1 million km 2 catchment of the Murray-Darling Basin (MDB), Australia. They are often implemented to enhance or maintain ecological outcomes of a natural flow, fresh, or flood (OEH, 2012). However, apart from methanogenesis in sediments (Boon & Mitchell, 1995;Boon et al., 1997), little is known about the role of environmental flows for planktonic metabolism and microbial diversity in semi-arid floodplain wetlands. Some previous research has investigated planktonic metabolism during environmental flow conditions in one of the largest wetland systems in the MDB, the Macquarie Marshes (Kobayashi et al., 2009(Kobayashi et al., , 2013(Kobayashi et al., , 2014 showing that GPP and PR are highly variable and that hydro-geomorphological setting can be a critical factor determining the balance of GPP/PR. For example, within the water-column