Based on the monthly average monitoring data of water quality from 19 sections in the Minjiang River Basin during the period from January 2014 to November 2015, we used the self-organizing map(SOM)and principal component analysis(PCA)to study the characteristics of temporal-spatial variations of water quality in the Minjiang River Basin, and conducted a comprehensive assessment of water quality of the Minjiang River with the water quality indices. Through the SOM analysis, we classified the water samples into three space groups, in which the water quality variation period was divided into two phases: one from April to November, and the other from December to March of the following year. The PCA analysis shows that the nutrients in the tributaries of the Shaxi and Futunxi rivers and in the urban river section in Fuzhou City downstream the Minjiang River maintained at a high level in the spring and winter. Meanwhile, the organic pollution level was high in some parts of the upper reaches and the downstream Minjiang River mouth in the spring and summer. The results of evaluation of water quality indices show that the water quality in the Minjiang River Basin is good on the whole. The three sub-basins and the lower reaches of the Minjiang River showed a descending order in water quality as follows: the Futunxi Basin, the Jianxi Basin, the Shaxi Basin, and the lower reaches of the Minjiang River Basin.