The Mekong Delta faces significant challenges in supplying Vietnam and its export market countries with agricultural commodities, while ensuring livelihoods and providing living space to its growing population in the context of climate change and the country’s agrarian transition. Anthropogenic factors, such as the construction of dykes to control river flooding, river sand mining, the further development of triple-cropping rice production, and infrastructure development, together with climate change impacts on sediment and water availability, are all combining to threaten agricultural production. One of the key challenges in sustainable development is the need to identify plausible future states of agricultural-based socio-ecological systems which draw upon differing strategies of land management, and to characterise the impacts of these systems on both the landscape and employment. It was hypothesised from the literature and rapid rural appraisals that each land system can only provide a certain number of jobs, which was further demonstrated using binomial regressions. We show that the odds of being employed are lower for intensive agricultural systems (OR=0.78 for triple rice; 0.91 for intensive aquaculture) than for diversified systems (OR=1.16 for rice-aquaculture; OR=1.63 for mixed fruit trees). Drawing from workshops with local and national stakeholders, we then used Earth observation and national census data in a spatial land use systems dynamic framework to simulate two alternative Mekong Delta futures based upon the climate pathway RCP 4.5 in combination with two existing policies (i) Resolution No. 124 (Specialisation) which promotes triple crop rice and aquaculture intensification and (ii) Resolution No. 639 (Diversification), which states that there should be a development of sustainable rice aquaculture and crop diversification. Based on the quantitative objectives of each policy, we estimated likely changes of services provided by land use systems if either policy were to dominate. The estimated impacts of each future scenario on the provision of employment ultimately indicate that policies with a diversification development paradigm will provide more employment (+0.9%) than policies with a specialisation paradigm (− 46%), and that current policies have potentially conflicting consequences. Decisions driving towards intensive farming risk triggering rural unemployment and outmigration, potentially exacerbating urban poverty in major cities such as Can Tho and Ho Chi Minh City. On the other hand, decisions aiming at increasing diversified agricultural systems can help secure more job opportunities. Our results indicate that spatial planning policies should rely on a broad-based assessment of land system services that include employment and environmental impacts to ensure a just transition towards resilient and environmentally sustainable rural territories.