Global rivers play a critical role in transporting, and biologically cycling, nutrients and organic matter from land to sea. But assessing these fundamental processes is complicated in braided rivers, where parallel water flows that fluctuate over both time and space. To-date scientific understanding of these rivers relies primarily on water quality measurements carried out only in the main channel. We tested the hypothesis that biological processing rates (and thus potential nutrient turnover) would be highest outside of the main channels, in slower flowing and shallow side braids and springs. In-channel ~continuous measurements of dissolved oxygen and temperature across multiple channels in an oligotrophic alpine braided river suggests that within-channel springs contribute up to 100x more to ecosystem respiration than the faster flowing main channel. We also report extreme levels of temporal variability in productivity in respiration over the year, with low flows and high temperatures combining to creates bursts of productivity (productivity/respiration = 12). These findings highlight the need for new approaches capable of integrating spatial fluctuations in order to accurately assess biogeochemical functioning in braided rivers.