Anthropogenic activities impacting marine environments are internationally recognized as welfare issues for wild cetaceans. This study validates a first evidence-based physical indicator for the welfare assessment protocol of humpback (n = 50) and fin whales (n = 50) living in a highly anthropized environment. Visual assessments of body condition, skin health, prevalence of injuries and parasite/epibiont loads were performed using a species-specific multi-scale measuring tool. A total of 6403 images were analyzed (fin, n = 3152; humpback, n = 3251) and results were validated through reliability and positive discrimination statistical tests. Based on physical measures, welfare assessment results showed that 60% of humpback whales were considered in a good welfare state compared to only 46% of fin whales. Significant relationships were observed in both species, between environmental parameters like dissolved oxygen levels, and prevalence of cutaneous lesions like pale skin patch syndrome. Furthermore, animals with injuries due to anthropogenic activities were more likely to be in poorer body condition, suggesting chronic stress affecting welfare.