The water quality in the Yangtze River has become worse from time to time, and thus to control the water quality and to protect the river have been a major issue for sustainable development in the region. In this paper, a model for the prediction of water quality in the river has been established, and this will provide reference values for any control measures to be taken for the protection of the water quality. First, by using the water quality data in 17 observation stations obtained within recent two years in the Yangtze River, a simple evaluation of the water quality in the river was conducted, and it is shown that the recent measures taken for the control of the water quality in the Yangtze River had some positive effect for improving the water quality. Second, the water quality data obtained from 1995 to 2004 in the Yangtze River were used, and the Markov transferred matrix is structured, with the Markov model established. The accuracy and the validity of the model were confirmed by the observed data. The water quality in the Yangtze River in the next ten years is then forecasted by the Markov model. That is, the standards I, II, III, IV water will reduce year by year, and the V, the poor standard V water will increase gradualy. To 2014, the kind I water in the Yangtze River only has 0.405 9 percent, the poor kind V water will be 26.2714 percent, the undrinkable water (namely IV,V and the poor V water) will reach 47.468 percent. Therefore, we must find a much more effective way to control deterioration of the water quality in the Yangtze River. Finally, through the computation, the smallest percentages of sewage water to be processed each year were obtained. The poor kind V water might be prohibited, and the kinds IV and the poor V water might be controlled in 20%, thus guaranteeing that we have enough drinkingwater source.