Suboptimal farm management can lead to (chronic) stress and can result in external morphological damage, which both can have deleterious effects on fish performance and welfare. This study is the first to investigate a potential correlation between chronic stress and the occurrence of external morphological damage in rainbow trout (Oncorhynchus mykiss) reared commercial flow through systems. To quantify chronic stress in eight different farms, scales of 10 fish per farm were sampled for scale cortisol analysis using UPLC-MS/MS. Measured external morphological damage of fish included damage to the eyes, skin and fins, as well as deformities and emaciation. Further, the influence of management (water supply, water supply per kg fish, total water exchange duration, average stocking density, feeding frequency) and water quality (oxygen, temperature, pH, ammonium, ammonia, nitrite, nitrate, turbidity) on chronic stress level and external morphological damage was assessed. Measured eye- and skin damage, deformities and emaciation occurred less frequently, while fin injuries were common and differed significantly in severity between farms. Results on all fish across farms showed a highly positive correlation between scale cortisol and total fin injury. A limited water supply, −supply per kg fish and −exchange as well as higher stocking densities and feeding frequencies resulted in a comparably reduced water quality, indicated by correlations with lower oxygen levels, higher levels of nitrogen compounds, higher temperature and turbidity. After conducting a principal component analysis, multiple linear regression models showed that scale cortisol was mainly predicted by total fin injury, temperature and the pH, ammonia and nitrite component. Total fin injury was majorly predicted by the management component concerning water supply, −supply per kg fish and −exchange duration as well as by stocking density, scale cortisol, the pH, ammonia and nitrite component and feeding frequency. Findings on scale cortisol support fin injuries to be an important welfare issue and suitable on-farm welfare indicator. Higher scale cortisol levels and higher fin injuries, directly and indirectly influenced by farm management, are indicative for impaired welfare and support the necessity of reducing chronic stress and the occurrence of fin injuries in aquaculture settings.