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The role of rainfall space-time structure, as well as its complex interactions with land surface properties, in flood response remains an open research issue. This study contributes to this understanding, specifically in small (< 15 km2) urban watersheds. Using a flood frequency analysis framework that combines stochastic storm transposition-based rainfall scenarios with the physically-based distributed GSSHA model, we examine the role of rainfall spatial and temporal variability in flood frequency across drainage scales in the highly-urbanized Dead Run watershed (14.3 km2) outside of Baltimore, Maryland, USA. The results show the complexities of flood response within several subwatersheds for both short (< 50 years) and long (> 100 years) rainfall return periods. The impact of impervious area on flood response decreases with increasing rainfall return period. For extreme storms, the maximum discharge is closely linked to the spatial structure of rainfall, especially storm core spatial coverage. The spatial heterogeneity of rainfall increases flood peak magnitudes by 50 % on average at the watershed outlet and its subwatersheds for both small and large return periods. The results imply that commonly-made assumption of spatially uniform rainfall in urban flood frequency modeling is problematic even for relatively small basin scales.