Effective waterfowl management relies on the collection of relevant demographic data to inform land-management decisions; however, some types of data are difficult to obtain. For waterfowl, brood surveys are difficult to conduct because wetland habitats often obscure ducklings from being visually assessed. Here, we used Unoccupied Aerial Systems (UAS) to assess what wetland habitat characteristics influenced brood abundance in Suisun Marsh, California, USA. Using a thermal-imaging camera, we surveyed 17 wetland units that encompassed 332ha of flooded area on the premises of seven waterfowl hunting clubs during the waterfowl breeding season. Additionally, using a combination of multi-spectral imagery collected from the UAS flights and LiDAR data from the previous year, we mapped habitat composition within each unit to relate to brood observation counts. From June 3–7, 2019, we identified 113 individual broods comprising 827 ducklings. We found a positive relationship between the number of broods observed and the proportion of the unit that was flooded. We also found a positive relationship between the number of broods observed and the area of effective habitat—a metric of flooded habitat within two times the 95th-percentile Euclidean distance that all broods were observed from any vegetated cover. Brood surveys using UAS could complement the traditional Breeding Population Survey and provide local managers with fine-scale and timely information about shifts in brood abundance in the region.