The subsidence pond is an important water resource for coal mining areas in China. In order to take full advantage of the subsidence pond, a floating photovoltaic cover or a pillaring photovoltaic cover were installed on the surface water of the subsidence pond in the Huainan coal field. Different photovoltaic systems (floating/pilling cover) equipped in the subsidence pond may affect the water quality; thus, assessing the metals in the subsidence pond with the solar photovoltaic system is of great importance for environment control. In this research, surface water samples were collected from three different subsidence ponds, with or without the solar photovoltaic system. The concentrations of Pb, Cr, Ni, Cu, As, Mn, and Zn in the water of the subsidence pond were determined using ICP-MS and AFS. Then, the health risk posed by the heavy metal in different subsidence pond waters via the ingestion pathway was evaluated and analyzed using the assessment model recommended by USEPA. The results indicated that the mean concentrations of Pb, Cr, Ni, Cu, As, Mn, and Zn in the water of different subsidence ponds were less than the environmental quality standards for surface water (China, Grade II). Cr showed a higher non-carcinogenic risk than the other metals, and the photovoltaic cover actually decreased the total non-carcinogenic risk in the photovoltaic subsidence pond compared with the natural subsidence pond. Non-carcinogenic risks of single and total heavy metals in the subsidence ponds with or without solar photovoltaic systems were below 1; thus, these risks in different subsidence ponds were considered to be at an acceptable level. However, the potential single carcinogenic risks of Cr, Ni, and As; and the multielement carcinogenic risks of Pb, Cr, Ni, and As exceeded the limits of 1 × 10⁻⁶ and 1 × 10⁻⁴, respectively, suggesting that these metals showed single and total potential health risks in the subsidence pond, with or without the solar photovoltaic system. Further, the subsidence pond with the photovoltaic cover showed higher total carcinogenic risks in comparison with the natural subsidence pond. Therefore, a subsidence pond with a solar photovoltaic system should be monitored periodically to ensure the water safety.