This work investigated the distribution, partitioning, and ecological risks of 16 polycyclic aromatic hydrocarbons (PAHs) in water and sediment of the Yinma River Basin in China in normal, wet, and dry seasons. Sixteen PAHs were analyzed in 17 paired sets of water and sediment samples collected from the study area. The concentrations of PAHs in water and sediment showed spatial-temporal variations, the concentrations in water ranged from 167.6 to 373.9 ng/L with a mean value of 227.9 ng/L in the normal season, from 186.0 to 386.9 ng/L with a mean value of 281.6 ng/L in the wet season, and ranged from 147.0 to 315.9 ng/L with an average value of 218.6 ng/L in the dry season, while concentrations in sediment varied from 895.6 to 2,518.2 ng/g with a mean value of 1,739.4 ng/g in the normal season, from 1,233.0 to 4,763.0 ng/g with a mean value of 2,122.6 ng/g in the wet season, and ranged from 914.2 to 5,678.5 ng/g with an average value of 1,943.7 ng/g in the dry season. Partitioning of PAHs in water and sediment was studied and the result showed that PAHs tend to absorb in sediment. Ecological risk assessments were conducted based on the species-sensitivity distribution (SSD) model, with results suggesting that ecological risks of individual PAHs in water and sediment were little, and the multiple congeners of PAHs in sediment from some sampling sites had ecological risks. Primary sources of 16 PAHs in water and sediment were identified with isomer ratios, and results indicated that primary sources of PAHs in water were identified as a mixture pattern of petroleum and combustion sources, and in sediment were identified as a mixture pattern of petroleum and grass, wood and coal combustion sources.