Study region: This study was carried out in the 32 km2 Birch Creek watershed in the Catskill Mountains of New York State. Birch Creek is situated within the Hudson River Basin. Study focus: Very few studies have paired measurements of changes in the extent of the actively flowing channel network with measurements of small scale flow variations. In this study, we map changes in a 23.5 km active channel network and concurrently take periodic measurements of discharge at 31 sub-channels (with drainage areas ranging from 0.04 to 11.5 km2) in order to better understand the spatial distribution of baseflow generation over time within the catchment. New hydrological insights: For the 31 different sub-channels, baseflow discharge per unit drainage area and per unit stream length were highly variable, even during periods of higher moisture storage when all channels were active. Simple mapping of the active channels would not have recognized these sizable spatial differences in discharge contribution. Previous studies of hydrologic scaling in the Catskills have noted the likelihood of heterogeneity in discharge below a threshold of approximately 3–8 km2. This study provides direct documentation of such heterogeneity at smaller spatial scales. When considering perennial and ephemeral streams, such heterogeneity was not well explained by standard topographic, geologic, or meteorological factors. We suggest the heterogeneity may arise from difficult to map fine-scale variations in subsurface properties.