Hydrology is the main driver of dissolved organic matter (DOM) dynamics in intermittent rivers and ephemeral streams. However, it is still unclear how the timing and the spatial variation in flow connectivity affect the dynamics of DOM and inorganic solutes. This study focuses on the impact of flow cessation on the temporal and spatial heterogeneity of DOM quantity and quality along an intermittent stream. We monitored a headwater intermittent stream at high spatial and temporal frequencies during a summer drying episode and analysed dissolved organic carbon (DOC) and its spectroscopic properties, inorganic solutes and dissolved CO. The drying period determined the disruption of the fluvial continuum with a recession of stream continuum at a rate of ~60 m/d and the gradual formation of a patched system of isolated pools of different sizes. Our results showed that the period of time that had elapsed since isolated pool formation (CI-days) was an essential factor for understanding how drying shaped the biogeochemistry of the fluvial system. Overall, drying caused a high DOC concentration and an increase in the humic-like fluorescence signal. Additionally, solutes showed contrasting responses to hydrological disconnection. Electrical conductivity, for instance, is a clear "sentinel" of the fragmentation process because it starts to increase before the hydrological disruption occurs. In contrast, DOC, most spectroscopic DOM descriptors and CO showed delayed responses of approximately 5-21 days after the formation of isolated pools. Furthermore, the spatial location and volume of each isolated pool seemed to exert a significant impact on most variables. In contrast, the temperature did not follow a clear pattern. These findings indicate that the fragmentation of longitudinal hydrological connectivity does not induce a single biogeochemical response but rather stimulates a set of solute-specific responses that generates a complex biogeochemical mosaic in a single fluvial unit.