Welfare assessments have risen to prominence in the aquaculture industry, with increasing awareness of their significance among stakeholders in Thailand. In this study, we conducted a welfare assessment of tilapia (Oreochromis spp.) farms in Thailand, focusing on health, environmental, behavioural, and nutritional indicators. Comparing semi-intensive (earthen ponds) and intensive farming practices (cage culture), we found significant differences in the overall health score, particularly at farm F due to a disease outbreak (Kruskal–Wallis, p = 0.01). Skin and fin scores varied across farms, indicating their potential as indicators of tilapia health. Environmental assessments revealed differences in transparency between the two culturing systems (Mann–Whitney, p = 0.02). During the harvesting process, tilapia behaviours indicated poor welfare across all farms. However, no statistically significant difference in overall welfare scores was found between the two culturing systems. Correlations were observed between nutritional, environmental, and health indicators, with negative correlations between fish density and water transparency (r = −0.87, p = 0.02), presence of inhabitants (r = −0.78, p = 0.04), feeding behaviours (r = −0.78, p = 0.04), and swimming behaviours during capture (r = −0.98, p = 0.001). These findings provide valuable insights to enhance tilapia-farming practices and welfare in Thailand.