Shallow waterbodies are abundant in many landscapes across the globe and are increasingly acknowledged for their role in freshwater C cycling. This study investigated organic-matter decomposition potentials in flocculent organic sediment, a rarely-investigated sediment type commonly found in shallow waters. Further, this study investigated how porewater chemistry and temperature affect decomposition rates within flocculent sediment. We quantified decomposition rates during 3 seasons by deploying a standardized substrate (cotton strips) within and above the flocculent sediment layer in the littoral zones of lakes, shallow through-flow wetlands, and depositional zones on the margins of stream channels of southwestern Michigan, USA. We then compared our results with those reported for other freshwater settings that used the same cotton-strip assay. There was high accumulation of organic matter in the shallow waterbodies, but decomposition rates in flocculent sediments averaged 1.7× greater than rates measured in oxic overlying waters and were generally only eclipsed by temperature-adjusted rates reported in streams, which are typically well-oxygenated, flowing environments. Rates were positively correlated with sediment porewater concentrations of soluble reactive P and dissolved iron and negatively correlated with ammonium. Warmer temperatures also resulted in increased decomposition rates, and the temperature sensitivity results suggest that decomposition rates in flocculent sediments could increase 11 to 52% with a 1 to 4°C increase in water temperatures, a realistic range of increase for this region in the next 100 y if climate change continues at the current pace. Thus, high organic matter inputs, rather than slow decomposition, must lead to the development of flocculent organic sediments. Future warming could therefore increase decomposition rates and tip the balance toward net losses of organic matter.