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Health of an ecosystem is very much important as we depend on its goods and services for our existence. Because of this, we need to continuously monitor its health for human benefit and for identifying areas for improvement of our natural systems. The present study tries to assess the condition of a coastal ecosystem within the Vembanad Lake, Kerala, India, using key water quality parameters at micro-level. Principal component analysis identified the minimum required water quality dataset for further analysis and was scored using linear scoring functions. The weighted additive method was used to integrate the individual scores to arrive at a final score representing the ecosystem health. Spline interpolation was applied to develop the ecosystem health map of the study area. Using this method, 35.8% area of the aquatic ecosystem studied was characterized as good, 32.2% as moderate, 26.2% as fair and 5.8% as poor. The assessment results can help the policymakers/managers to make appropriate decisions for the better management of the coastal ecosystems studied. Moreover, this methodology can be replicated for the assessment of coastal regions with similar ecosystem characteristics. [ABSTRACT FROM AUTHOR]