This study analyzed the fate and transfer of PAHs through multiple media in Dianchi Lake and the sediment records of polycyclic aromatic hydrocarbons (PAHs) in sediments. The model simulation results showed the simulated concentrations to be in good agreement with the measured values. The concentration and total amount of PAHs were the highest in the sediment, which is an important sink for PAHs in lake systems. The main transport direction of the PAHs in the three phases was from the atmosphere to the water to the sediment. Advection and emission inputs were the primary input pathways for PAHs in the atmosphere, and advection output was the main removal path. The main input sources pathways for PAHs in sediments was the sedimentation of particulate matter in water, with diffusion and degradation being the primary methods of removal. Advection and atmospheric dry and wet deposition were the main sources of PAHs in water, with particulate deposition being the primary removal process. The range of PAHs was 336–3520 ng/g in sediments in Dianchi Lake, with an average of 1569 ng/g, peaking in 2012. Among the predicted future PAH concentrations in the sediments under the five shared socioeconomic pathways (SSPs), the lowest PAH concentration was found under SSP3 from 2025 to 2035, whereas the lowest PAH concentration was found under SSP4 from 2035 to 2050. In the sustainable path of SSP1, although the concentration of PAH pollutants showed an increasing trend in the short term, the increase in PAHs concentration in sediments slowed in the long run.