Pond culture, as a major component of aquaculture, is one of the important sources of agricultural source pollution. Pollutions from pond culture has been a big threat in the Taihu Basin, where with dense water network and developed fisheries. Hence, to reduce the eutrophication of water bodies, and to restore water quality and health, it is important to control the discharges of nitrogen, phosphorus, chemical oxygen demand and other pollution sources during pond culture. Based on field sampling survey and remote sensing interpretation, this study combined with GIS software to estimate the pollution load of pond culture in the Taihu Basin. The results showed that discharges of total nitrogen (TN), nitrate nitrogen (NO₃^--N), ammonium nitrogen (NH₄⁺-N), total phosphorus (TP), dissoluble phosphorus (DP) and chemical oxygen demand (COD_Cr) in the Taihu Basin during 2014-2015 were 6.1×10⁶, 1.1×10⁶, 1.7×10⁶, 1.3×10⁵, 1.1×10⁵ and 8.0×10⁷ kg, respectively. The discharge factor of the above pollutions for fish ponds were 69.5, 12.4, 20.1, 1.6, 1.3 and 919.8 kg/ha, shrimp ponds were 3.0, 0.5, 0.9, 0.07, 0.06 and 39.3 kg/ha and crab ponds were 6.4, 1.2, 1.9, 0.2, 0.1 and 84.9 kg/ha. All of the pollutions from fish pond culture were much higher than those of shrimp and crab pond culture. The distribution characteristics of various pollution sources in pond culture in this basin were similar. The pollution discharge in the northwest, south and northeast of the Lake Taihu was higher in most areas than those in the east and southwest of it. Factors such as the well-developed pond farming industry and high fertilizer input result in high pollution discharge from ponds in this basin. Therefore, we proposed some reduction measures to control pond culture pollution in this basin, these could also be referenced by other basins.