Metabolic processes are critical for carbon cycling and trophic dynamics in rivers and wetlands. Gross primary productivity of phytoplankton (GPP) and planktonic respiration (PR) – together, aquatic ecosystem metabolism – fluctuate spatially and over time due to variations in channel morphology, flow, inundation, nutrients, microbial diversity, and other factors. The balance of GPP:PR determines whether an aquatic ecosystem exhibits net autotrophy (i.e. carbon consumption) or net heterotrophy (i.e. carbon production). Rivers tend to be viewed as efficient transport pathways of energy, and they act as meta-ecosystems and downstream conveyors of organic carbon in the landscape. However, we question generally accepted models of biophysical controls on carbon flux in rivers when systems suffer from major biophysical disturbances, or do not exhibit commonly assumed downstream trends in biophysical conditions and processes. We draw on examples from inland and coastal catchments of New South Wales to highlight 1) the role of channel enlargement as a disturbance mechanism, and 2) non-conformity of longitudinal biophysical conditions in rivers with significant wetlands, both of which appear to significantly effect aquatic ecosystem metabolism within in-channel habitats. Our findings show that 1) GPP and PR can be enhanced in enlarged reaches leading to a dominance of PR and greater heterotrophy than in intact reaches; and 2) downstream changes in GPP and PR do not necessarily lead to persistent increases in PR and declines in net ecosystem production (GPP – PR), rather, that distinct peaks, troughs and threshold values of GPP and PR can be identified and are important. While we know that the short-term response of carbon, nutrients and planktonic communities to flow and inundation can be highly variable, there is a pressing need to characterise the variability of and relationships between hydrological, geomorphological and biological conditions in rivers and wetlands, as well as their abiotic controls.