In terms of quality particularly difficult to describe are processes of mass exchange between different phases (e.g., atmospheric air-water, water-river sediment, water-algae, etc.). Whitman's model is most often used to describe the mass transport processes through the phase boundary. Theoretical analysis of the mass transfer process through the phase boundary showed that in unsteady states, the calculation results obtained from Whitman's model differ from the results obtained using the accurate diffusion model. These differences are due to the fact that concentration profiles in the direction of diffusion process change in time. Assumptions for Whitman's model do not include changes in the concentration distribution over time. Therefore, the correction factor was introduced to Whitman's model. The correction factor is defined as a parameter that multiplies a concentration derivative over time in the mass transport model. The correction factor can be used to estimate the effective diffusion coefficient of the substance that permeates from the aqueous phase to the sediment. The correction factor improves the degree of fit of the mass transport model to the measurement data. It can be used to estimate the effective turbulent diffusion coefficient from water phase to the sediment phase.