Water and tufa samples were collected from Arrow Bamboo Lake, the stream from Panda Lake to Five-Color Lake, Pearl Shoal and Shuzheng Lakes in Jiuzhaigou National Nature Reserve, China, between October 2013 and September 2014, to investigate tufa growth rate and water environment (water temperature, pH, electric conductivity, major ions and nutrients), and analyzed to explore the main causes of tufa degradation. The mean annual rate of tufa growth was low and varied within lakes, with the maximum deposit thickness of 332 µm/y. The calcite saturation index ranged from 0.65 to 0.83. Scanning electron microscope images showed that the tufa deposits had non-isopachous structures, and diatoms were the dominant microorganisms that participated in tufa deposition. Porous and crystalline structures of deposits were linked with a high tufa growth and small amounts of diatoms. Conversely, tufa deposits with amorphous and loose structures showed a low crystal growth rate and a high number of diatoms. A one-way analysis of variance and a least significant difference test were applied to identify site differences in water chemistry. Linear correlations indicated that nitrate, phosphate and sulfate inhibit tufa growth (p < 0.05). Increased nitrogen and phosphorus concentrations that originate mainly from atmospheric pollution and tourist activities at scenic attractions could trigger excessive diatom growth, which inhibits tufa precipitation. A series of measures should be implemented (e.g., the visitor number and vehicles should be regulated and controlled) to minimize tufa degradation in the Jiuzhaigou National Nature Reserve.