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A field survey was conducted during flow pulses to investigate the longitudinal spatial patterns in water quality, dissolved inorganic and organic matter, phytoplankton, planktonic bacteria, zooplankton, gross primary productivity (GPP) of phytoplankton and planktonic respiration (PR) in channels of the large floodplain system (similar to 124 km in length) of the Macquarie Marshes, south-eastern Australia. Four river reaches (areas) with distinct hydrogeomorphological characteristics within the distributary zone of the lower Macquarie River were chosen for analysis of abiotic and biotic variables in their in-stream environments. The results showed marked longitudinal spatial variation in the values within and among the measured environmental variables including such functional aspects as primary productivity and PR. The variables that tended to have increasing values in a downstream direction were conductivity, total nitrogen (TN), total phosphorus (TP), dissolved reactive phosphorus (DRP), dissolved silica, dissolved organic carbon (DOC), dissolved organic nitrogen (DON), dissolved organic phosphorus (DOP), ratio of DOC/DON and counts of planktonic bacteria. Conversely, the values that tended to decrease downstream were the ratios of TN/TP, DIN/DRP, DOC/DOP, DON/DOP and GPP/PR. Variables that had a localized peak(s) were dissolved oxygen, turbidity, dissolved inorganic nitrogen, GPP, PR and counts of cyanobacteria, diatoms, green algae, cryptomonads, protozoans, rotifers, copepods and cladocerans. Overall, two distinct ecological zones were identified within the broader distributary functional process zone (FPZ): these being the upstream zone with relatively high levels of DO, turbidity, diatoms and GPP/PR ratio, and the downstream zone with relatively high levels of nutrients, dissolved organic matter, cyanobacteria, planktonic bacteria, protozoans and cladocerans. The results of this study describe the spatial connectivity of ecological processes related to hydrogeomorphological factors within a FPZ of a riverine ecosystem, and support the predictions of the riverine ecosystem synthesis framework that ecological patterns and processes can be discontinuous on a longitudinal spatial scale. Copyright (C) 2010 John Wiley & Sons, Ltd.