Dissolved organic carbon (DOC) concentrations vary among headwaters, with variation typically decreasing with watershed area. We hypothesized that streamflow intermittence could be an important source of variation in DOC concentrations across a small watershed, through (a) temporal legacies of drying on organic matter accumulation and biotic communities and (b) spatial patterns of connectivity with DOC sources. To test these hypotheses, we conducted three synoptic water chemistry sampling campaigns across a 25.5‐km2 watershed in south‐eastern Idaho during early spring, late summer, and late fall. Using changepoint analysis, we found that DOC variability collapsed at a consistent location (watershed areas ~1.3 to ~1.8 km2) across seasons, which coincided with the watershed area where variability in streamflow intermittence collapsed (~1.5 km2). To test hypothesized mechanisms through which intermittence may affect DOC, we developed temporal, spatial, and spatio‐temporal metrics of streamflow intermittence and related these to DOC concentrations. Streamflow intermittence was a strong predictor of DOC across seasons, but different metrics predicted DOC depending on season. Seasonal changes in the effects of intermittence on DOC reflected seasonal changes from instream to flowpath controls. A metric that captured spatial connectivity to sources significantly predicted DOC during high flows, when DOC is typically controlled by transport. In contrast, a reach‐scale temporal metric of intermittence predicted DOC during the late growing season, when DOC is typically controlled by instream processes and when legacy effects of drying (e.g., diminished biological communities) would likely affect DOC. The effects of intermittence on DOC extend beyond temporal legacies at a point. Our results suggest that legacy effects of intermittence do not propagate downstream in this system. Instead, snapshots of spatial patterns of intermittence upstream of a reach are critical for understanding spatial patterns of DOC through connectivity to DOC sources, and these processes drive patterns of DOC even in perennial reaches.