The inter-provincial transboundary area of the Taihu Lake Basin is characterized by a complex river network and reciprocating flow. Frequent environmental pollution events in recent years have become a major safety hazard for the water quality in the Taihu Lake Basin. There are few early warning systems for environmental pollution events in China, the ability to simulate risk is insufficient, and systematic research on technology, development, and application is lacking. Thus, water management requirements are not met in the inter-provincial transboundary area of the Taihu Lake Basin. This paper proposes a cross-border risk management plan for pollution sources in the transboundary areas of the Taihu Lake Basin and an early warning and emergency response system for water pollution events using modern information technology. We used this system to assess and classify 2713 risk sources for nitrogen and phosphorus pollution into 5 categories. We simulated the discharge of a pollutant into a tributary and the early warning and emergency response for the transboundary region. The results indicate that the proposed early warning and emergency response system substantially improved the transboundary water environment and lowered the risk of pollution in the Taihu Lake watershed.