As a class of persistent organic pollutants (POPs), polycyclic aromatic hydrocarbons (PAHs) have mutagenic, teratogenic, and carcinogenic effects, so they can pose a greater threat to the natural environment and human health. Most of the PAHs in coal mining areas originate from the mining and utilization process of coal resources, which has a variety of carriers in the environment: atmosphere, water bodies, soil, sediments, etc. To study their pollution status in the subsidence waters of the Huainan coal mining area, sixteen priority control PAHs of sixteen surface water samples from seven subsidence water bodies were tested using gas chromatography–mass spectrometry (GC–MS), and their pollution characteristics were analyzed. Overall, the concentration of PAHs ranged from 212 to 283 ng·L−1, and benzo[b]fluoranthene (BbF) had the highest average concentration. In addition, the concentration of PAHs above four rings was relatively high. After statistical analysis, the Pearson correlation coefficient calculation showed a highly significant positive correlation between PAHs with the same number of rings. Three principal factors were selected using factor analysis, which could explain 88.37% of the total variance, to conduct the source identification. Coal combustion was found to be the main source of PAH pollution in the area. Then, ecological risk using the risk quotient (RQ) method was carried out. The results showed that PAH contamination was medium risk, among which, benzo[a]anthracene (BaA) and BbF had a high ecological risk. In addition, the results of biological toxicity evaluation using the species sensitivity distribution model (SSD) showed that benzo[a]pyrene (BaP) had a high proportion of potential effects on aquatic organisms. By using the response addition model, the evaluation results showed that the ecological risk of the subsidence water bodies in the Panyi mine was the highest. Finally, human health risks were evaluated from two pathways: dermal contact and ingestion. The carcinogenic health risks from the dermal contact exceeded the permissible limits, while the hazard entropy of non-carcinogenic risks from the above two pathways were less than 1.