The urban, industrial and agricultural growth of the cities across Taubaté region influences water quality of Paraíba do Sul river. Due to the importance for human life quality, economic development and environmental sustainability it is necessary to keep water quality control of this river. In this study, physical, chemical and biochemical attributes of rice cultivation were analyzed in the Paraiba do Sul river water in the Taubaté region. The analyses were made during the rice growing season. The results showed that the practice of rice cultivation increased the pollution level of Paraíba do Sul river. Due to rice cultivation, fertilizers and organic matter were introduced in the river waters demonstrating that fertilization practices require rigid control for wetland rice production.