This study aimed to explore the effects of a notable increase of suspended sediment content in aquaculture water on the immune and antioxidant capacity of rainbow trout as well as the microbial community on the body surface. The sediment from the Yellow River was used and maintained suspended using the pump pool cycle and blower aeration method. Three suspended sediment content gradient groups of 0, 1000, and 10000 mg/L were set up for the rainbow trout acute stress test. The activity changes of alkaline phosphatase (AKP), lysozyme (LZM), total superoxide dismutase (T-SOD), peroxidase (POD), catalase (CAT), and malondialdehyde (MDA) in serum were detected continuously after stress culture, as well as the differences of skin and gill microbial communities after 7 days of stress culture. The results showed that the activity of AKP and LZM in the rainbow trout serum significantly changed within 3–6 h after the acute increase of sediment content, but then the stable state was gradually restored. T-SOD and POD decreased and increased, respectively, within 24 h of sediment stress, but they all returned to a steady state after 48 h. CAT increased significantly after stress, with no significant dependence on sediment content. MDA decreased significantly after stress, and it was dependent on sediment content. On the body surface of rainbow trout, Bacteroidetes and Proteobacteria were the dominant bacteria groups; however, the number and richness of microorganisms in the skin mucus were significantly higher than those in the gill tissue. The tissues sites tested revealed a significant increase in the relative abundance of Acidovorax, Pseudomonas, and Chryseobacterium compared to the control group under suspended sediment stress (P＜0.05). The relative abundance of Sphingobacterium decreased significantly (P＜0.05). The results above indicate that the acute stress of suspended sediment can disrupt the immune and antioxidant capacity of rainbow trout in a short period and increase the harmful microorganisms on their body surface.