Previous studies have shown that moderate concentrations of Chinese tallow leaf litter can quickly reduce dissolved oxygen and pH in the aquatic environment. While these studies mostly focus on its effects on the performance of amphibians, this study focuses on determining the causes of deoxygenation and acid water. We also examined the effects of Chinese tallow litter on other water quality parameters and how changes may influence microbial communities in aquatic environments. We used laboratory and outdoor experiments to demonstrate the effects of Chinese tallow litter on aquatic chemistry. Additional laboratory studies investigated litter quality and soluble nutrients. We tested the effects of an antimicrobial agent on microbial activity in Chinese tallow litter treatments. Outdoor mesocosms were used to assess the impact of Chinese tallow and native litter monocultures on aquatic chemistry and microbial community composition. We measured water chemistry and sampled mesocosms for microbial rRNA genes. We found evidence that biological mechanisms are causing deoxygenation, while chemical mechanisms may be influencing acid water. Chinese tallow litter was of different quality, decomposed faster and leached more soluble nutrients than native species. Chinese tallow litter traits appear to have different effects on microbial activity and community composition than native litter. Our results suggest that Chinese tallow litter can have an impact on aquatic chemistry and the composition of aquatic microbial communities as it replaces native species in southern forests. The implications of our results are potential shifts in aquatic ecosystem processes.