Set pair analysis (SPA) is emerging as a new system theory method for analyzing vagueness and uncertainty of facts. Many problems of uncertainty of fuzziness can be solved with the application of identity-discrepancy-contrary expression, and five-element connection number (FECN) is an extension of SPA. Aiming at the problem being too complex for the present evaluation methods on lake eutrophication, an assessment of lake eutrophication based on situation of five-element connection number was suggested. The results of the assessment are basically in concordance with other evaluation methods. So, the evaluation model provides realistic support for remediation-related decisions for water resource management.