A numerical dye is used to track freshwater released in May and June from the Mississippi and Atchafalaya rivers using a hydrodynamic model. These months are chosen because discharge and nutrient load in May and June is significantly correlated with an area of the Texas–Louisiana continental shelf affected by seasonal bottom low dissolved oxygen. Results show that the two different river sources influence different parts of the region affected by hypoxia, so that both rivers appear to contribute to forming the hypoxic region. Analysis shows that both nutrient loading and stratification caused by freshwater fluxes from the rivers are consistent with the distribution of dyed freshwater in late July.