Water pollution is an increasingly important issue in the world and in Vietnam. Currently, there have been many studies on water quality to assess the risk of water pollution with different approaches. This article focuses on the use of MASSFLOW theory - a mass flow analysis method - to assess the level of pollution in water sources. Through the open source software STAN, the article builds 5 scenarios to assess the risk of water pollution for the Quan Lo - Phung Hiep irrigation system - one of the irrigation systems that plays an important role in the Mekong Delta region with discharge from shrimp ponds in the area. The research results increase the accuracy in assessing the risk of water pollution, contributing to supporting the planning of water resources management and proposing more effective measures to control pollution sources. This not only contributes to environmental protection but also generates sustainable economic benefits for both communities and enterprises.