In order to approach the characteristics of nitrogen and phosphorus pollution caused by cage culture and the balance of nitrogen and phosphorus during the process of cage culture, a monitoring was conducted in Daya Bay of Guangdong Province, China from April 2002 to Jane 2003. The results show that the concentrations of total nitrogen (TN) in the waters at the sites with five and ten years of cage culture history are 1.8 and 2.3 times of that at control site respectively. Ammonium (NH3-N) is the main form of nitrogen in spring while nitrate (NO3-) in winter. The concentrations of TN, total dissolved nitrogen (TDN) and dissolved organic nitrogen (DON) are highest in autumn. The concentration of phosphorus increases with the increasing of the culturing time, among which phosphate (PO34-) increases most obviously.The concentrations of total phosphorus (TP) and total dissolved phosphorus (TDP) are highest in autumn. The nitrogen and phosphorus are accumulated significantly in the sediment of cage culture area. The model of N balance in the cage culture area: bait (70.62%) + fry (0.28%) + input by tide (14.8%) + release from sediment (14.3%) = harvest of adult fish (12.07%) + deposition into sediment (28.75%) + output by tide (56.18%) + others (3.00%). The model of P balance: bait (83.11%) + fry (0.17%) + input by tide (12.23%) + release from sediment (4.49%) = harvest of adult fish (8.43%) + deposition into sediment (48.59%) + output by tide (41.94%) + others (1.04%). In one fish growth year, the contents of nitrogen and phosphorus in harvest of adult fish are only 17.0% and 10.1% of the contents of nitrogen and phosphorus in fish bait and fry, wherein 83% of nitrogen and more than 89% of phosphorus in fish bait became marine pollutants.