ABSTRACT The intestinal tract is an important functional organ in fish, as it plays a key role in digestion and absorption, mucosal immunity, endocrine function, and metabolism. Therefore, damage to this organ greatly impacts fish health. This injury is usually associated with a poor aquaculture water environment, stressful conditions, and pathogen presence. In this review, in light of gut injury being a common pathology in aquaculture, we have summarized the current understanding of the intestinal damage of fish caused by carbonate water stress, and the mechanism of intestinal tissue damage caused by carbonate saline water stress, including the intestinal barrier function of fish and the role of various cells and molecules involved in the occurrence and development of diseases. Comparative data on carbonate stress responses across different teleost lineages (such as the Cyprinidae and Perciformes) have been integrated. The review also covers current methods for treating intestinal damage in fish, including dietary interventions, medications, and probiotics. Our findings highlight the need for more in‐depth research in this area to better understand the mechanisms underlying the occurrence of intestinal tissue damage in fish in carbonate‐based saline waters and to develop effective preventive and therapeutic strategies. Improved development of saline–alkaline waters and research into new treatments are essential for the sustainability of aquaculture and the health and productivity of farmed fish.