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Abstract Stream dissolved organic matter (DOM) is a globally important carbon flux and a locally important control on stream ecosystems, and therefore understanding controls on stream DOM fluxes and dynamics is crucial at both local and global scales. However, attributing process controls is challenging because both hydrological and biological controls on DOM are integrated and may vary over time and throughout stream networks. Our objective was to assess the patterns and corresponding controls of diel DOM cycles through a seasonal flow recession by using reach‐scale in situ sensors in a non‐perennial stream network. We identified five characteristic diel variations in DOM with differing phase and amplitude. During snowmelt flows, diel variations in DOM were consistent among sites and reflected diel flowpath shifts and photodegradation. Evapotranspiration‐driven diel stage oscillations emerged at two upstream sites, shaping diel DOM patterns indirectly, by creating conditions for instream DOM processing. At a spring‐fed site, minimal diel variation was observed throughout the summer whereas at an intermittent reach, daily drying and rewetting created biogeochemical hot moments. This research demonstrates that controls on DOM vary over time and space, even in close proximity, generating asynchronous fDOM patterns during low flows, illuminating shifts in biogeochemical processes and flowpaths.