With decreasing water availability as a result of climate change and human activities, analysis of the influential factors and variation trends of chlorophyll a has become important to prevent reservoir eutrophication and ensure water supply safety. In this paper, a structurally simplified hybrid model of the genetic algorithm (GA) and the support vector machine (SVM) was developed for the prediction of monthly concentration of chlorophyll a in the Miyun Reservoir of northern China over the period from 2000 to 2010. Based on the influence factor analysis, the four most relevant influence factors of chlorophyll a (i.e., total phosphorus, total nitrogen, permanganate index, and reservoir storage) were extracted using the method of feature selection with the GA, which simplified the model structure, making it more practical and efficient for environmental management. The results showed that the developed simplified GA-SVM model could solve nonlinear problems of complex system, and was suitable for the simulation and prediction of chlorophyll a with better performance in accuracy and efficiency in the Miyun Reservoir.