Large-scale estimations of flood losses are often based on spatially aggregated inputs. This makes risk assessments vulnerable to aggregation bias, a well-studied, sometimes substantial outcome in analyses that model fine-grained spatial phenomena at coarse spatial units. To evaluate this potential in the context of large-scale flood risk assessments, we use data from a high-resolution flood hazard model and structure inventory for over 1.3 million properties in Massachusetts and examine how prominent data aggregation approaches affect the magnitude and spatial distribution of flood loss estimates. All considered aggregation approaches rely on aggregate structure inventories but differ in whether flood hazard is also aggregated. We find that aggregating only structure inventories slightly underestimates overall losses (−10% bias), and when flood hazard data is spatially aggregated to even relatively small spatial units (census block), statewide aggregation bias can reach +366%. All aggregation-based procedures fail to capture the spatial covariation of inputs distributions in the upper tails that disproportionately generate total expected losses. Our findings are robust to several key assumptions, add important context to published risk assessments and highlight opportunities to improve flood loss estimation uncertainty quantification.