Estrogens are known to have an adverse impact on the reproductive functions of aquatic animals in natural waters. However, the estrogen levels are usually below the detection limits and vary drastically in the surface water, making it difficult to assess the environmental exposure in watershed management. While dynamic models are useful to bridge the data gaps on estrogen levels in surface water, the complex interconversion among estrogens hinders the accurate calculation of estrogens levels. To address the issue, we developed a kinetic model consisting of three first-order ordinary differential equations to track the concentration change of three key estrogens, estrone (E1), 17α-estradiol (E2α), and 17β-estradiol (E2β) with time resulting from the complex interconversion process. The model was solved by the matrix method and applied to 15 sets of lab data measured both in anaerobic and aerobic conditions as well as in aqueous solutions and solids with various initial estrogen concentrations from earlier studies. The coefficient of determination (R2) values for those datasets range between 0.842 and 0.989, indicating very good accuracy for the application to the natural environment. This kinetic model can help managers to assess the environmental exposure in watershed management and make determinations on effective solutions.