This study identifies stakeholders’ perceptions of ecosystem services (ESS) along the Mekong River in Vietnam. It evaluates trade-offs made between ESS under different Pangasius catfish development scenarios, and stakeholders’ preferences to these scenarios. The study was conducted through interviews, focus group discussions and a questionnaire survey with 150 households. Rice cultivation and Pangasius catfish farming were identified as the most important economic activities. Provisioning services were scored as the most important ESS, followed by supporting, regulating and cultural services. Most stakeholders perceived that an intensification of Pangasius catfish farming would increase the production of catfish, but decrease nine other ESS, while integrated Pangasius catfish farming would decrease the Pangasius catfish production but increase nine other ESS. An integrated system was preferred by the majority of the respondents, mainly because it was perceived to enhance several ESS and provide benefits to local communities. In conclusion, a sustainable development of Pangasius catfish farming in the Mekong Delta must include local stakeholders’ participation and apply farming strategies that make use of the natural environment without severely or irreversibly degrading it.