Three water bodies of different functionalities, i.e., undeveloped (A), aquaculture (B), and aquatic vegetable planting (C), in Lake Houhu unstable coal mining subsidence area, were studied to address the distribution and migration of nitrogen and phosphorus in a column system of overlying water column, sediment pore water and sediments. The results showed that the contents of nitrogen and phosphorus were quite different in different sediment-water interface. The concentrations of nitrogen and phosphorus in overlying water column were in the order of A>B>C. Although no significant difference in concentrations of nitrogen and phosphorus in pore waters of these three water bodies were observed, they were distinctly higher than those in overlying water columns. This suggested an upward migration of nitrogen and phosphorus from pore waters to overlying water columns. The highest concentrations of nitrogen and phosphorus were examined in the sediments of aquatic vegetable planting water body. Overall, the study found that water bodies were polluted by nitrogen but had limited availability of phosphorus.