Diurnal variations of hydrochemistry were monitored at a spring and two pools in a travertine-depositing stream at Baishuitai, Yunnan, SW China. Water temperature, pH and specific conductivity were measured in intervals of 5 and 30 min for periods of 1 to 2 days. From these data the concentrations of Ca2+, HCO3−, calcite saturation index, and CO2 partial pressure were derived. The measurements in the spring of the stream did not show any diurnal variations in the chemical composition of the water. Diurnal variations, however, were observed in the water of the two travertine pools downstream. In one of them, a rise in temperature (thus more CO2 degassing) during day time and consumption of CO2 due to photosynthesis of submerged aquatic plants accelerated deposition of calcite, whereas in the other pool, where aquatic plants flourished and grew out of the water (so photosynthesis was taking place in the atmosphere), the authors suggest that temperature-dependent root respiration underwater took place, which dominated until noon. Consequently, due to the release of CO2 by the root respiration into water, which dominated CO2 production by degassing induced by temperature increase, the increased dissolution of calcite was observed. This is the first time anywhere at least in China that the effect of root respiration on diurnal hydrochemical variations has been observed. The finding has implications for sampling strategy within travertine-depositing streams and other similar environments with stagnant water bodies such as estuaries, lakes, reservoirs, pools and wetlands, where aquatic plants may flourish and grow out of water.