The invention provides a water environment and water ecology safety guarantee management system, which comprises a safety evaluation model, a risk evaluation model, a crisis early warning model, a water level water quality biomass supervision model, a sudden accident emergency response planning model, a post-accident evaluation model, a safety guarantee measure module and a comprehensive treatment module. Therefore, the water environment and water ecology safety guarantee management system belongs to an overall situation guarantee treatment management system realizing the potential safety hazard identification, the weak link early warning, the key element supervision, the sudden accident emergency handling and the post-accident evaluation and analysis, and the key monitoring and the prevention pertinence on key elements and key regions with potential safety hazards are enhanced, so the comprehensive management on the water environment and water ecology safety of monitored water regions can be enhanced; and in addition, the full-area balance supervision costs of the water environment and water ecology are effectively reduced, the supervision efficiency on the water environment and water ecology is improved, and the important significances of guaranteeing the water environment and water ecology safety of lakes and promoting the harmonious development of the social economy and the ecological environment are realized.