River health monitoring traditionally has made use of structural measurements (water quality or taxonomic composition of aquatic organisms). We argue that a more complete assessment of river health should include functional metrics, such as rates of organic matter decomposition and ecosystem metabolism. Leaf breakdown links the characteristics of riparian vegetation with the activity of both aquatic invertebrates and microbial organisms and is affected by natural and human-induced variation in a wide range of environmental factors. Measurement of leaf breakdown is relatively simple and has modest equipment requirements. River metabolism (gross primary productivity and ecosystem respiration) measures the rates of production and use of organic C in river ecosystems as a whole, providing a direct estimate of the food base that determines life-supporting capacity. Metabolism measurements require more sophisticated equipment than do measurements of leaf breakdown, but improvements in technology have made metabolism measurements relatively easy. We review the factors that influence leaf breakdown and river metabolism and pay particular attention to the effects of human-induced environmental stressors. We also describe how measurements can be standardized and suggest criteria for interpreting functional measures in terms of river ecosystem health. Last, we consider the strengths and weaknesses of both methods as functional measures and provide recommendations for their use as biomonitoring tools.