Composite Water Quality Identification Index (CWQII) and multivariate statistical techniques were used to investigate the temporal and spatial variations of water quality in Honghu Lake. The aims are to explore the characteristics of water quality trends in annual, monthly, and site spatial distribution and to identify the main pollution factors. The results showed that the values of CWQII increased from 2.0 to 4.0 from the years 2001 to 2005, then decreased from 2006 and kept a balance between 2.0 and 3.0 from 2006 to 2011, indicating that the water quality of Honghu Lake deteriorated from 2001 to 2005 and has gradually improved since 2006, which were likely achieved after water protection measurements taken since 2004. The monthly change rules of water quality were influenced by a superposition of natural processes and human activities. In samples numbered 1-9 from upstream to downstream, the maximum values of CWQII often occurred in sample site 9 while the minimum ones often occurred in sample site 2, indicating that the water quality near the upstream tributary was the poorest and that in the core zone was the best. Incoming water from the trunk canal of the Sihu area upstream was the largest pollution source. The sensitive pollution nutrients were mainly caused by the total nitrogen, followed by the total phosphorus.