Light intensity has an important environmental influence on the quality and yield of aquatic products. It is essential to understand the effects of light intensity on water quality and fish metabolism before large-scale aquaculture is implemented. In this study, two low-intensity light levels, 0 lx and 100 lx, were used to stress Nile tilapia (Oreochromis niloticus), with a natural light level (500 lx) used as control. The pH, dissolved oxygen and ammonia contents were significantly lower in the water used in the 0 lx and 100 lx groups than in controls, while the levels of nitrite and total phosphorus were apparently higher. Moreover, the numbers of heterotrophic bacteria, Vibrio and total coliforms in aquaculture water were 157.1%, 314.2% and 502.4% higher, respectively, after 0 lx light stress for 15 days. The survival rate of Nile tilapia decreased significantly to 90.6% under 0 lx light on the 15th day. Of the immune-related genes, the expressions of IFN-γ, IL-12 and IL-4 were 390.3%, 757.8% and 387.5% higher under 0 lx light and 303.3%, 471.2% and 289.7% higher under 100 lx light, respectively. These results indicate that low-intensity light changes the physicochemical parameters of aquaculture water and increases the number of bacteria it hosts while decreasing the survival rate and increasing the disease resistance of Nile tilapia.