The timing and composition of organic matter (OM) inputs to rivers are important as carbon plays a major role in river functioning. Management of Australian rivers since European settlement has altered inputs of organic matter to these systems. Heterotrophic microbes play a critical role in the transformation of OM in rivers, allowing transfer of carbon to other biota. Alteration to the proportions of OM from different sources affects microbial functioning due to differences in OM composition. Macrophytes can represent important sources of carbon to rivers, however their inputs and in-stream processing are poorly understood. The aim of my study was to examine inputs and microbial processing of macrophyte OM in Australian lowland rivers under different flows. Distributions of dominant macrophytes (Typha orientalis, Phragmites australis, Vallisneria gigantea and Persicaria prostrata) were mapped in three lowland river reaches in south eastern Australia. Integration with flow data in a GIS allowed the determination of macrophyte inundation patterns under different flows. Resource allocation (biomass and nutrients), live and dead shoot densities and litter production were monitored in the field over 18 months. DOM release from different macrophyte tissues was examined in the laboratory and leachate composition was assessed using nutrient and spectral analyses. Responses of riverine microbial communities to different OM sources were assessed from substrate-induced respiration and enzyme activity experiments and field measurements of respiration and enzymatic responses to varied OM inputs. Finally, all data were integrated into a model of microbial responses to macrophyte OM inputs induced by different flows. Large populations of macrophytes occurred at all three sites, at bed level, on in-channel benches and on banks. Bank slope, channel heterogeneity and the vertical distribution of macrophyte beds all affected macrophyte inundation patterns. Substantial differences in biomass allocation, nutrient dynamics and litter composition were observed among different plant growth forms and over time. While leaves represented the major shoot component in litter for all species, stems and reproductive structures were also important in some species. Aside from the litter pool, translocation to rhizomes represented a major sink for annual production in emergent plants. Patterns of shoot density and litter production over time varied among species, providing a source of variation for particulate, and hence dissolved OM inputs upon inundation. The majority of DOM release from POM occurred within 24 hours of inundation. Growth form, tissue type (blade, stem, etc.) and status (live or dead) affected rates, quantities and composition of DOM release, with implications for microbial utilisation. Both overall activity and patterns of carbon utilisation in riverine microbes changed in response to altered OM inputs. Patterns of microbial carbon use were shown to be specific to the carbon source which induced them. Modelling showed that flow regulation had a major impact on OM inputs and microbial metabolism, through the effects of flow variability on macrophyte vertical distributions, macrophyte bed inundation and dilution. Positive relationships between discharge, DOM inputs and microbial metabolism were observed at the most highly regulated site (drought < current < historic < flood). While a similar pattern occurred at the less regulated site in terms of total loading, dilution effects resulted in a reversal of this trend on a reach volume basis. Microbial metabolism and DOM inputs were restricted to summer/autumn under regulated flows compared to a greater emphasis on winter/spring inputs and microbial activity under unregulated flows. Continual OM inputs during winter with pulsed inputs in spring under natural flows probably benefit larger, slow-growing macro-invertebrates. River regulation promotes pulsed macrophyte OM inputs during spring/summer, potentially favouring riverine microbial and zooplankton production, although at lower levels due to the overall reduction in OM inputs. The predictive model of macrophyte OM inputs and microbial responses developed throughout this thesis represents a major step forward in our understanding of macrophytemicrobe interactions and our ability to manage our river systems. This work has shown that flow manipulation can be used to influence macrophyte organic matter inputs to rivers and microbial responses, affecting whole stream metabolism and food web interactions.