Pond ecosystem not only provides essential agricultural irrigation and washing water, but also stores rainwater in rainy seasons. However, the pollution status of pond system around Poyang Lake was seldom studied. Here, we investigated the water and sediment chemical characteristics, phytoplankton and benthic macroinvertebrates, as well as habitat conditions of 23 rural ponds around Poyang Lake. Results showed that water quality of 91.3% rural ponds was inferior V (National Surface Water Environmental Quality Standard of China) with the main pollutants of total nitrogen (TN) and total phosphorus (TP). In rural ponds, fifty-nine species of phytoplankton and nineteen benthic macroinvertebrates were identified, Cyanophyta and Chlorophyta were the dominant phytoplankton groups, and oligochaetes and aquatic insects were the most dominant taxa among all benthic macroinvertebrates. And an integrated evaluation system based on chemical, biological and physical index was set up to assess the pollution status of rural ponds. According to the composite integrity index, 2 rural ponds (8.70%) were classified as Very poor, 9 rural ponds (39.13%) were classified as Poor, 9 rural ponds (39.13%) were classified as Fair, and 3 rural ponds (13.04%) were classified as Good. And the composite integrity index in 4 counties followed the sequence of Xingzi County (0.598, Fair) > Jinxian County (0.425, Fair) > Xinjian County (0.379, Poor) > Nanchang County (0.335, Poor). Therefore, measures should be taken for improving the water quality, habitat conditions and biotic community of rural ponds, especially for the severely polluted rural ponds in Xinjian and Nanchang County.