In the Mekong delta, intensive shrimp farming rely heavily on a wide panel of antibiotics (ABs) to prevent disease epidemics. Consequently, large amounts of antibiotic multi-resistant bacteria are emerging, threatening adjacent aquatic habitats used for irrigation and drinking water, and potentially impairing human health. In this study, quantification of AB resistance genes (ARGs) was carried out for two consecutive years along the Vam Co River (Long An Province, Viet Nam), a river receiving several effluent channels from intensive shrimp farms. qPCR analyses were conducted on resistance genes sul2 (sulfonamide), oxa1 (ß-lactams), ermB (erythromycin), as well as on intl1 (Class1 integrons) and on bacterial 16S rRNA genes. Results showed that resistance genes and Class 1 integrons were present in all river compartments (sediment and water). Both sul2 and oxa1 reached highest abundances. For instance, sul2 reached respectively a maximum of 5.9×104 copies per gram and 1.3×104 copies per mL of sediment and water. Ratio between 16S rRNA and oxa1 showed that up to 5.1% of all bacterial cells may harbor this resistance gene in water samples. Distribution patterns of both genes were constant along the course of the river, an indication of the generalized use of the related ABs in the shrimp cultures. Contrariwise, strong seasonal and local fluctuations were found for ermB, denoting a more limited and localized usage of the related AB. In conclusion, massive presence of ARGs along the river confirmed that both water and sediment are dissemination routes, stressing for the development of alternative farming practices.