This study evaluates whether lionfish (Pterois volitans) population dynamics vary across reef systems and time periods associated with environmental disturbance at Banco Capiro and La Ensenada. Specifically, we assess temporal variation in aggregation size, relative abundance, and sex-based population structure across three periods (2014-2016, 2017-2019, and 2023-2024), encompassing coral bleaching events including Tela’s 2023 mass mortality event. At La Ensenada, median aggregation size remained consistent, although variability declined. Banco Capiro showed stable aggregation patterns, though significant temporal shifts were detected (p < 0.001), indicating aggregation changes. Relative abundance (lionfish per dive) differed between reefs: Banco Capiro exhibited a significant increase in 2023-2024 relative to earlier periods (p < 0.001), La Ensenada showed no significant change (p = 0.40). Sex-based analysis showed males were significantly more abundant than females at both sites. At La Ensenada, sex was a strong predicator of lionfish type (p < 0.001), while year had no effect. At Banco Capiro, both year and sex were significant predicators (p < 0.001), indicating temporal shifts in population structure. These findings demonstrate site-specific variation in lionfish dynamics and suggest that environmental disturbance, including coral bleaching and mass mortality may influence invasive predator behaviour and abundance through site-dependant ecological processes.