Stress in farmed fish is associated with poor feeding, slow growth, disease, and mortality. Therefore, it is essential to closely monitor the stress levels in fish to optimize farming practices which could then enhance productivity and welfare in aquaculture operations. Cortisol, a stress hormone that can be found in the blood, is a reliable biomarker for evaluating fish stress. As blood sampling is highly invasive, alternative cortisol sampling methods such as fin, mucus, and the surrounding water which contains released cortisol, have been proposed as less invasive or non-invasive sampling methods. However, a comprehensive understanding of their temporal dynamics and associations with plasma cortisol levels is still lacking. In this study, we subjected Lates calcarifer, Asian sea bass within a farm-scale (3,000 L tank, 9,000 L system) high-flow rate (8,000 L/hour) Recirculating Aquaculture System (RAS) to an acute handling stress challenge specifically involving chasing and air exposure, and quantified cortisol dynamics both within different biological samples including blood, fin, and mucus and in tank water from multiple sampling points. We showed that handling stress induced an expected increase in plasma and mucosal cortisol, peaking at 4 hours and 24-48 hours, respectively, and that plasma and mucus cortisol were moderately correlated, especially during the stress period. Fin cortisol did not show consistent dynamics. Water cortisol similarly rose, but peaked within 40 minutes from the start of the stressor, in a pattern that was dependent on the site of sampling within the RAS system, likely due to RAS circulation dynamics. Our study is the first to examine the impact of stress on cortisol accumulation and release in Asian Sea bass in a farm-scale RAS, thus providing insights that complement existing research on the efficacy of fin, mucus, and water cortisol as stress indicators that could help optimize aquaculture productivity and welfare.