<p>The Seven Maar Lakes of San Pablo, Philippines are vital freshwater resource of ecological, economic and cultural importance. However, due to the anthropogenic activities taking place, ecosystem health is being compromised. Thus, there is a need to regularly assess water quality for conservation and protection. One approach for a simple, effective and comprehensive water quality assessment is through calculating water quality index wherein it transforms complex water quality data into a single dimensionless number. With this, the research aimed to utilize different water quality index methods to characterize the ecosystem health of the Seven Lakes of San Pablo. This study utilized two water quality index methods—weighted arithmetic water quality index (WAWQI) and modified CCME-water quality index (MCWQI). Based on the resulting indices, ecotourism lakes (Mohicap, Pandin and Yambo) were categorized as good to very good classification. While aquaculture lakes (Bunot, Calibato, Palakpakin and Sampaloc) were classified from fair to poor conditions. This result was supported by the K-means clustering which grouped the lakes together. Correlation analysis showed that WAWQI had strong negative correlation with phosphorus while MCWQI had strong negative correlation with BOD. Comparing the two methods, WAWQI is more responsive to the presence of pollutants which makes it more appropriate since this index could reflect specific pollutant impacts more strongly and can provide stricter water quality classification necessary for conservation and protection. Overall, the utilization of water quality index method reflected the ecosystem health condition which could be used as a basis for water quality management of the Seven Lakes of San Pablo.</p>