Wetlands are rich ecosystems recognized for ameliorating floods, improving water quality, and providing other ecosystem benefits. This part of a two-paper series presents a relatively detailed process-based model for nitrogen and phosphorus retention, cycling, and removal in flooded wetlands. The model captures salient features of nutrient dynamics and accounts for complex interactions among various physical, biogeochemical, and physiological processes. The model simulates oxygen dynamics and the impact of oxidizing and reducing conditions on nitrogen transformation and removal, and approximates phosphorus precipitation and releases into soluble forms under aerobic and anaerobic conditions, respectively. Nitrogen loss pathways of volatilization and denitrification are explicitly accounted for on a physical basis. Processes in surface water and the bottom-active soil layer are described by a system of coupled ordinary differential equations. A finite-difference numerical scheme is implemented to solve the coupled system of ordinary differential equations for various multiphase constituents' concentrations in the water column and wetland soil. The numerical solution algorithm is verified against analytical solutions obtained for simplified transport and fate scenarios. Quantitative global sensitivity analysis revealed consistent model performance with respect to critical parameters and dominant nutrient processes. A hypothetical phosphorus loading scenario shows that the model is capable of capturing the phenomenon of phosphorus precipitation and release under oxic and anoxic conditions, respectively