Photochemical reactions in the water environments are essential for understanding the fate of organic pollutants, which exist widely in aquatic environments causing potential risks. Therefore, this study aimed to integrate a module of the photodegradation process into a vertically one-dimensional model of the lake to quantify the influence of phytoplankton on the photodegradation process for the first time. After adjusting the code of the APEX (Aqueous Photochemistry of Environmentally occurring Xenobiotics), the suite of photochemical reactions was integrated into the pollutant module of MyLake (Multi-year Lake simulation), as MyLake-Photo. This integrated model was then applied to calculate the concentration of four organic micropollutants under the ranges of solar radiation conditions (0–390 W/m2), phytoplankton biomass (0.01–20 mg/m3 of chlorophyll), and water temperature (1–25 °C). These scenario analyses revealed that phytoplankton biomass and pollutant photodegradation are negatively correlated owing to the light absorption by chlorophyll. Thermal stratification also significantly influenced the vertical distribution of organic micropollutants. Then, the model was applied for calculating a temporal distribution of ibuprofen concentration in Lake Giles (PA, USA) with a simple but realistic assumption. The concentration of organic micropollutants varies with seasons, which was mainly affected by the changes in irradiance and water temperature. In this manner, the integrated model is capable of estimating the temporal and vertical shifts of the concentration of organic micropollutants in lakes, allowing us to investigate the fate of organic micropollutants in lakes. The integrated model also allows us to investigate the effect of phytoplankton and CDOM on the photodegradation of organic micropollutants, which should be combined with field surveys and experimental studies for further improvement.