This paper aims to calculate and analyze the spatial and temporal variations in the groundwater flow quantity in Nam Co Lake based on the water balance principle. The results show that a large amount of groundwater was gradually lost and that, groundwater loss decreased from 1.9 billion m³ to 1.5 billion m³ from the period of 1980–1984 to 1995–2009. The comparative analysis in the current study indicates that the decrease in the groundwater index has a strong linear relationship with the temperature of the ground surface on the Tibetan Plateau, with a correlation coefficient as high as 0.92. Moreover, environmental variations such as large-scale engineering construction projects and increases in water storage may have played dominant roles in the sudden changes in the water quantities of plateau lakes (e.g., Nam Co Lake) during the periods of 1990–1995 and 2000–2009. The increased water levels resulted in reduced groundwater losses, which may lead to the substantial expansion or gradual shrinkage of the Qinghai–Tibet Plateau lakes over short periods of time. The results of this study provide an important reference for studying the mechanisms of lake water level changes on the Qinghai–Tibet Plateau.