According to the urgent requirement of water quality monitoring, water bloom prediction and emergency treatment decision-making, a multi-functional information system based on GIS (Geographic Information System) is designed and developed, which integrates water quality monitoring and analysis, water bloom prediction and emergency treatment decision-making. VS2010 platform and SQL Server 2005 database are used in the system, and the remote data communication is realized by GPRS. The system has functions such as lakes and reservoirs’ water quality real-time monitoring, teletransmission and location, water quality data analysis, water bloom prediction and emergency treatment decision-making. The medium-term prediction of water bloom is realized by wavelet neural network, and the optimal choice of water bloom emergency treatment decision-making projects is realized by multi-attribute decision-making theory. This design offers effective decision-making system for environmental protection departments, which also has significant meaning to the protection and renovation of water environment, and its application and promotion have considerable social and economic benefits.