Transformations from artisanal fishing to aquaculture are now ubiquitous in many small-scale coastal fishing communities worldwide, often in response to the economics of fisheries and climate change. Understanding the long-term dynamics of community livelihoods is an important step in designing appropriate fishery management and adaptation policies to navigate the effects of such transformations. The literature has focused predominantly on addressing snapshots of livelihood conditions, with less attention being paid to how present conditions have emerged over time, and for whom. Using an integrated analytical approach, this study investigates the longitudinal livelihood trajectories in two small-scale fishery villages around the Tam Giang Lagoon in Vietnam, with particular attention paid to the changes since the introduction of aquaculture in the late 1980s. Three distinct livelihood trajectories — accumulating, fluctuating, and marginalising — represent the differential pathways available to fishing- and aquaculture-dependent households. In this constrained yet shared resource space, the transformational adaptation through aquaculture has benefitted the adopters and enhanced their livelihood resilience; yet, it has had detrimental consequences for the artisanal fishers who find themselves locked into a state of heightened vulnerability. The findings provide evidence of differential and unintended consequences of new adaptations to livelihood struggles in small-scale fishery communities, and they point to the need for well-targeted policies to reduce rather than exacerbate growing inequalities. Fishery management policies and interventions in this lagoon, and similar contexts, need to take into account the heterogeneity in livelihood trajectories and unequal social vulnerability to inform more just adaptation strategies and improve the wellbeing of fishery communities.