Assessing the health of rivers and lakes is crucial for ensuring water security and promoting sustainable development. Building upon previous research, this study employs an enhanced CRITIC-entropy weight method to calculate the index weights within a health assessment system for plateau rivers and lakes. Evaluations were conducted on the Nyang River and Zari Namco Lake, revealing the former’s health status as “healthy” with criterion layer weights assigned to social service function, “basin”, “water”, and biology in descending order. Zari Namco achieved a “very healthy” status, with criterion layer weights ordered as “water”, “basin”, biology, and social service function. The findings indicate a need for improvement in the Nyang River’s riparian vegetation width and shoreline stability, while Zari Namco requires enhancements in shoreline natural conditions, macrobenthic organism integrity, and lake trophic status. The paper concludes with several recommendations for the protection and management of both the Nyang River and Zari Namco Lake.