Aquaponics is a sustainable eco-agricultural technology that combines aquaculture with horticulture. However, there is still limited research on the effects and preventive measures of acid rain on aquaponics vegetables. Herein, we conducted an experiment to decipher the combined effect of acid rain (pH 5.0, 4.0, and 3.0) and the protecting treatments (AR and AG) on the lettuce, in which plant growth, photosynthetic system, antioxidant system, nutrition and mineral elements were investigated. The results indicated that acid rain was the main factor affecting the growth of lettuce. Without acid rain, the various indicators of lettuce did not alter under AR and AG treatments. As pH decreased, lettuce yield and quality gradually decreased. Acid rain stimulated the antioxidant system and reduced root vitality and nutrient absorption. AG treatment mitigated the harm of acid rain on lettuce root vitality, soluble sugars, nitrate, and ascorbic acid content. At pH 4.0, AG treatment had the greatest mitigating effect. While at pH 3.0, AG treatment had no effect on the SOD activity, total phenolic and soluble sugar content of lettuce. These findings indicated that protecting the roots can mitigate the impact of acid rain on the edible and nutritional value of aquaponics lettuce. As pH decreased, this mitigating effect gradually diminished. In summary, the detrimental effect of acid rain on aquaponics lettuce was inevitable, yet protective root treatments offered a viable strategy to mitigate this stress. This research established a foundation for the enhancement of aquaponics systems resilience to acid rain.