Thirteen water quality parameters from 12 monitoring stations were collected to study the effects caused by climate and anthropogenic activities on water quality in 2003 in Daya Bay, South China Sea. The data matrix has been built according to the results, which were analyzed by fuzzy c-mean cluster (FCM) and cluster analysis (CA). This analysis has identified anthropogenic effects and seasonal characters of water quality. The dry and wet seasonality have been demonstrated with FCM and CA. The precipitation and the Southeast Asian monsoons, northeasterly from October to the next April and southwesterly from May to September have also an important influence on water quality in Daya Bay. In the spatial pattern, two groups have been classified with FCM and CA. Cluster I consisted of the sites S3, S8, S10 and S11 in the west and north coastal parts of Daya Bay. Cluster I is mainly related to anthropogenic activities such as fish-farming. Cluster II consisted of the rest of the stations in the center, east and south parts of Daya Bay. Cluster II is mainly related to seawater input from South China Sea. Thus, fuzzy c-mean cluster and cluster analysis can be an important tool for the successful characterization of regional-scale water quality.