Background: Salinity intrusion into coastal regions is an increasing threat to agricultural production of salt sensitive crops like paddy rice. In the coastal Mekong Delta, farmers respond by shifting to more salinity tolerant agricultural production systems such as alternating rice-shrimp and permanent shrimp. While shrimps are sensitive to pesticide residues used on rice, the use of antibiotics in shrimp farming can cause contamination in rice crops. These patterns of cross-contamination are not well documented empirically in the rapidly changing agricultural landscape. Objective and methods: Our objective was to understand changing pollution patterns induced by shifts in agricultural land use system. We addressed this by i) documenting pesticide and antibiotic use in three different agriculture land use systems (permanent rice, alternating rice-shrimp and permanent shrimp), and by ii) determining residues of pesticides and antibiotics in top soil layers of these three land use systems. Samples were taken in Sóc Trăng and Bến Tre province in the Mekong Delta, Vietnam. Chemical analyses comprised 12 of the most commonly used pesticides in rice paddies and six common antibiotics used in shrimp production. Results: Results showed that residues of pesticides were present in all agricultural land use systems, including shrimp aquaculture. Active ingredients were mostly fungicides with a maximum concentration of 67 μg kg−1 found for isoprothiolane in permanent rice systems, followed by alternating rice-shrimp and permanent shrimp systems. Furthermore, antibiotics were present ubiquitously, with fluoroquinolones accumulating to larger amounts than sulfonamides and diaminopyrimidines. All concentrations were below critical lethal threshold values. Conclusion: Overall, farmers were most conscious of agrochemical use in alternating rice-shrimp systems to prevent harm to shrimps, which was reflected in overall lower concentrations of agrochemicals when compared to rice systems. Thus, alternating rice-shrimp systems present a low risk option in terms of food safety, which may bring additional benefits to this so far rather low-input system in brackish water transition zone.