To understand water quality degradation during hypoxia, we need to understand sediment oxygen fluxes, the main oxygen sink in shallow hypolimnia. Kinetic models, which integrate diffusion and consumption of dissolved oxygen (DO) in sediments, usually assume a downward flux of DO from the sediment−water interface (SWI) with a zero-flux condition at the lower boundary of the oxic sediment layer. In this paper, we separately account for the oxidation of an upward flux of reduced compounds by introducing a negative flux of DO as a lower boundary condition. Using in situ measurements in two lakes, kinetic models were fit to DO microprofiles using zero-order and first-order kinetics with both zero and non-zero lower boundary conditions. Based on visual inspection and goodness-of-fit criteria, the negative-flux lower boundary condition, −0.25 g O2 m−2 d−1, was found to more accurately describe DO consumption kinetics. Fitted zero-order rate constants ranged from 50 to 510 mg L−1 d−1, and first-order rate constants ranged from 60 to 400 d−1, which agree well with prior laboratory studies. DO fluxes at the SWI calculated from the simulated profiles with the negative-flux lower boundary condition also showed better agreement with the observed DO fluxes than the simulated profiles with the zero-flux lower boundary condition.