Antibiotics are extensively applied in aquaculture for the treatment of microbial infections and to improve production. Among various antibiotics, sulfonamides (SA) are popular in fish farming, and SA residues in the aquatic environment have detrimental effects on both ecosystem and human health. Understanding the fate of SA in the aquatic environment is a basic necessity to provide an approach for solving the current problem. In this study, a two-dimensional lattice Boltzmann model was introduced to investigate the transport and occurrence of SA in Laizhou Bay, a prosperous aquaculture area in China. The model is based on the shallow-water equations and advection-diffusion equation with the Bhatnagaar–Gross–Krook scheme. Experimental data are used to verify the model after numerical simulations and the results illustrate the accuracy of the proposed model. This model provides a potential universal method for the simulation of the fate of antibiotics in the aquatic environment.