Coastal sediments adjacent to urban centers often receive high loads of organic matter (OM) due to large nutrient inputs from land that stimulate algae blooms. Early diagenetic models describing the remineralization of this OM in sediments have been developed for 50 years. Although these models can be applied to a range of marine sediments, specifying their model parameter values is difficult. In this study, one of the early diagnetic models was applied to simulate sediments in Osaka Bay, Japan and the polynomial chaos expansion (PCE) technique was used in order to choose optimal model parameters in the model. Following a sensitivity analysis, we estimated values for six parameters including the ratio of fast-decaying OM to total OM, the ratio of non-degradable OM to total OM, and the carbon–nitrogen ratio. Optimal parameter values were determined by minimizing the misfits between simulated and observed release rates of ammonium and phosphate from the sediments, and vertical profiles of inorganic nitrogen, and phosphorus in the porewater. Simulations with the optimized parameters successfully reduce a dimensionless root mean square error by 68% and agree better with the observed profiles and release rates than without parameter estimation.