The Prairie Pothole Region (PPR) of North America is a globally important area hosting >50 % of North America’s breeding ducks. Ducks in the PPR depend on wetlands and grasslands which have experienced accelerated losses in extent and quality due to agriculture. While other bird populations have declined, duck abundance reached record highs recently (2013–2017). We explored this discontinuity by examining monitoring data for trends in pond numbers (wetlands with ponded water) and interannual dynamics (water-level dynamics indexed by interannual change in pond numbers) and how those factors influenced duck productivity in the PPR during 1976–2019. Over time, pond numbers increased but their interannual dynamics declined, indicating stabilization of an ecosystem evolved with a dynamic climate. Our models accounted for 67 and 71 % of variation in productivity of PPR-obligate gadwall (Mareca strepera) and redheads (Aythya americana), respectively. Breeding productivity of these sentinel species was positively correlated with pond abundance and dynamics, and systematically declined. Accordingly, our analyses revealed sensitivity of breeding ducks to systematic change in the PPR previously obscured by increasingly abundant pond numbers. Interannual pond dynamics improved duck productivity and pond dynamics have declined indicating a de facto 44-year decline in duck productivity which is likely driven by water-level stabilization decreasing quality of brood-rearing wetlands. Residual temporal effects indicated that productivity has also declined for other reasons, such as agricultural land use changes. While mechanisms behind these correlations are speculative, they demonstrate the importance of further understanding land use and climate changes in the PPR for conservation of these important species and ecosystems.