Organic matter decomposition and ecosystem metabolism, which includes both gross primary production (GPP) and ecosystem respiration (ER), are good functional indicators of stream health. Decomposition of organic matter in streams is caused by a number of biotic and abiotic factors and directly integrates with microbial assemblages, energy conversion and fauna. Ecosystem metabolism indicates how much organic carbon is produced and consumed in an ecosystem and provides an indication of the life supporting capacity of a stream ecosystem. In summer 2019, we conducted a survey of 27 streams in Southland, New Zealand to assess the sensitivity of functional indicators as a measure of stream and river health. The rate of organic matter decomposition was estimated using a cotton strip tensile loss assay, while ecosystem metabolism was estimated using the open-channel, single-station regression method over 13 to 17 days. Tensile loss of cotton strips ranged from 0.04 to 6.53 %/d. GPP ranged from 1.4 gO2/m2/day to 22.3 gO2/m2/day, of all sites measured 23 (85%) fell into the satisfactory to healthy condition for GPP. ER ranged from 1.0 gO2/m2/day to 25.6 gO2/m2/day and 19 (70%) sites fell into the satisfactory to healthy condition for ER. Ecosystem metabolism measurements have shown that 85% of the studied sites oxygen uptake through respiration was higher than oxygen production, suggesting that organic matter from the surrounding catchment maintains the ecosystem food chain. Both cotton strip tensile strength loss and stream metabolism varied widely among stream sites, suggesting potential use of these assays to detect variation in watershed-scale environmental conditions.