River-lake connecting system (RLCS) plays an important role in controlling lake eutrophication due to its special geographical position and ecological significance. In addition, the pattern of phytoplankton variation and interaction between chlorophyll α and environmental variables are important for eutrophication management. To understand general water environment characteristics, including relationships between chlorophyll α and environmental variables in the Taige Canal-Taihu Lake system, a comparative study was conducted based on a two-year-long field investigation. This system was divided into a river region and a lake region based on cluster analysis. Investigated field data in the two regions were analyzed separately with principal component analysis (PCA) and stepwise multiple regressions for the relationships among water quality parameters. The spatial variation between the two regions can be found both in patterns of water quality parameters and relationships among them. Multivariate analysis showed that total phosphorous, chlorophyll α, and transparency were the main indicators of the spatial variations between the two regions. Relationships among water quality parameters showed that temperature and transparency were the primary environmental factors limiting phytoplankton growth in the river region. However, in the lake region phytoplankton may uptake phosphorus from sediments and its growth was limited by nitrogen during high-temperature seasons. Based on these characteristics, we suggested that reduction of nitrogen input and control of internal phosphorous loading was important for management of eutrophication in the studied area.