Small-scale aquaculture is essential to balance environmental health, economic growth, and social equity. However, the increasing frequency of Harmful Algae Blooms (HABs), commonly known as red tides, present a significant risk to both aquatic ecosystems and human well-being, threatening the productivity of the sector. This study investigates the impact of HAB-induced closures on mussel farming in Chile, the world's second-largest mussel industry, with a focus on how farm size influences resilience and adaptive capacity. With a 19-year dataset (2003-2021) covering small (<3 ha), medium (3-8 ha), and large (>8 ha) mussel farms, we analysed the temporal and spatial distribution of HAB closures and their effects on mussel export volumes. Using Generalized Additive Mixed Models (GAMMs), we reveal that small farms, while attempting rapid post-closure recovery, are more vulnerable to prolonged economic stress, primarily due to limited access to adaptive resources and fluctuating market prices. Larger farms, on the other hand, demonstrate a delayed but stable recovery, benefiting from superior spatial positioning and access to capital. While the industry showed sustained growth at the regional level, our analysis demonstrated an asymmetric, size-dependent pattern on local responses, where small producers are more vulnerable to unexpected climatic events and market fluctuations. Given the increasing frequency of HABs due to climate change, our findings underscore the need for equitable governance in the blue economy to prevent widening inequalities between small and large producers. Policy recommendations include enhanced monitoring systems, increased access to financial and technical resources for small-scale farmers, and market diversification to improve resilience against environmental disruptions.