Tourism remains one of the top threats in nature reserves worldwide. In this study, we first used both a field survey and in situ nutrient enrichment experiments to assess the effects of tourisms on aquatic ecosystems in a World Natural Heritage site that includes lakes, streams, shoals, and waterfalls. The results showed that phosphorus (P) enrichment altered benthic algal assemblage composition and the color of bryophyte-dominated benthic substrates in a shoal. Epilithic diatoms and their responses to the nutrient addition were significantly different between the control and test sites on a lake, which had contrasting tourist impacts in a lake. Second, we assessed the resilience of a lake heavily visited in the reserve by comparing phytoplankton density before and after a 2-year reserve closure due to an earthquake. Our study confirmed the hypotheses: (1) the perceived color change in Jiuzhaigou Natural Reserve waters was caused by nutrient enrichment in relation to tourist activities and was closely associated with a shift in algal composition; and (2) the changes to the fluvial and lake systems are still at their early stages and could be recovered by reducing tourism pressure. Our findings provide managers of protected karstic nature reserves with critical information for identifying causes of reserve degradation, estimating the carrying capacity for tourism and establishing limits of acceptable ecosystem changes.