Rivers are biodiverse ecosystems that play an essential role in the processing of organic matter from headwaters to the lower reaches. The biodiversity within these spatially complex ecosystems is often subject to huge seasonal variation, particularly in temperate regions, for example seasonal peaks in emergence of aquatic insects or migration of fish through the river network. However, these ecosystems are also subject to strong anthropogenic pressures that affect not only the biodiversity within this system, but the functions this biodiversity provides to key ecosystem processes. Therefore, spatial and temporally dynamics must be considered to effectively assess and understand the biodiversity and functioning within an ecosystem. Here, we assessed ecosystem function at a high spatial and temporal resolution across a large river network, specifically focussing on standardised organic–matter decomposition. Our results show—even when correcting for temperature—significant effects of both season and water chemistry parameters on microbial decomposition. However, we found no effect of space (i.e., site location within the network) on ecosystem function, contrary to expectations. We also found no imprint of the microbial community richness assessed in the water column (α–diversity and Shannon Index) on the patterns of organic–matter decomposition, however, this may be due to our focus on potential colonising microbes rather than benthic communities. Our study highlights the need to include functional indicators for the assessment of ecosystems.