Widespread use of neonicotinoid insecticides in North America has led to frequent detection of neonicotinoids in surface waters. Despite frequent surface water detection, few studies have evaluated underlying sediments for the presence of neonicotinoids. Thus, we sampled water and sediments for neonicotinoids during a one-year period at 40 floodplain wetlands throughout Missouri. Analyzed for six common neonicotinoids, sediment samples consistently (63% of samples) contained neonicotinoids (e.g., imidacloprid and clothianidin) in all sampling periods. Mean sediment and aqueous neonicotinoid concentrations were 1.19 μg kg^–1 (range: 0–17.99 μg kg^–1) and 0.03 μg L^–1 (0–0.97 μg L^–1), respectively. We used boosted regression tree analysis to explain sediment neonicotinoid concentrations and ultimately identified six variables that accounted for 31.6% of concentration variability. Efforts to limit sediment neonicotinoid contamination could include reducing agriculture within a wetland below a threshold of 25% area planted. Also, prolonging periods of overlying water >25 cm deep when water temperatures reach/exceed 18 °C could promote conditions favorable for neonicotinoid degradation. Results of this study can be useful in determining potential routes and levels of neonicotinoid exposure experienced by nontarget benthic aquatic invertebrates as well as potential means to mitigate neonicotinoid concentrations in floodplain wetlands.