The importance of information system evaluation has increased according to ICT development and this evaluation is required for objective verification. The aim of this study is to develop evaluation indicators for web-based information system and verify the availability of these evaluation indicators through applying to agricultural water integrated information system. This study finds and provides eight evaluation items and 64 indicators for a web-based information system using 3×3 Mandal-Art matrix that is a tool for creating creative ideas. These evaluation items are design, contents, navigation, stability, community, convenience, usefulness, and accuracy. Total 64 evaluation indicators were presented by deriving eight evaluation items for each using 9×9 Mandal-Art matrix. When evaluating information system using evaluation indicators, it can be identified the vulnerable items in the information system. Also, the comprehensive results of the information system could be understood when appearing a single score after weighting. In addition, it can also help to prepare a questionnaire for evaluation systematically.