1. Measurements of ecological patterns are often used as primary biological indicators of river health. However, these patterns provide little information about important stream ecosystem processes (e.g. the sources and fate of energy and nutrients). The direct measurement of these processes is considered fundamental to the determination of the health of stream and river ecosystems.
2. In this paper we used two basic approaches to assess stream ecosystem response to catchment disturbance and, particularly, to the loss of riparian vegetation in different forested biomes across Australia. Benthic gross primary production (GPP) and respiration (R24) provided measures of the amounts of organic carbon produced and consumed within the system, respectively. Stable isotope analysis was used to trace the fate of terrestrial and instream sources of organic matter in the aquatic food web. In a focal catchment in SE Queensland, additional measurements were taken of riparian attributes, catchment features and water quality.
3. Baseline measurements of GPP and R24 from undisturbed forest streams provided reference values for healthy streams for comparison with sites where the catchment or riparian vegetation had been disturbed. These values of metabolism were low by world standards in all biomes examined. Preliminary data from the Mary River catchment in SE Queensland indicated that these parameters were sensitive to variations in riparian canopy cover and, to a lesser extent, catchment clearing, and predictive models were developed. The ratio P : R (GPP : R24) was used to determine whether sites were net consumers (P < R) or producers (P > R) of carbon but this was not considered a reliable indicator of stream health on its own.
4. Although forest streams were typically net consumers of carbon (P < < R), stable isotope analysis of metazoan food webs indicated a high dependence on inconspicuous epilithic algae in some biomes.
5. A dramatic decline in the health of forest streams was observed when GPP substantially exceeded R24, especially when instream primary producers shifted from palatable unicellular algae to prolific filamentous green algae and macrophytes. These sources of instream production do not appear to enter aquatic food webs, either directly through grazing or indirectly through a detrital loop. Accumulation of these plants has led to changes in channel morphology, loss of aquatic habitat and often a major decline in water quality in some of the streams studied.