The dissolved organic matter (DOM) compositions in lake water have been widely studied; however, it is not clear how salinity fluctuations in brackish lakes with reeds affect DOM transformation in pore water. This experiment included three salinity groups (1,200 mg/L, 3,600 mg/L, and 6,000 mg/L) to research the interactions between bacteria and DOM in sediments under a salinity gradient. The results showed that higher salinity reduced the Fmax of protein-like substances and resulted in DOM becoming more aromatic and endogenous. Salinity affected DOM compositions due to the responses of functional bacterial communities. Thiobacillus was salt-tolerant and dominated in the sediments, the relative abundances of which were negatively correlated with the Fmax of the protein-like components. The relative abundance of Flavobacterium showed a positive correlation with salinity and a negative correlation with the Fmax of fulvic acid-like and tryptophan-like components. Pseudomonas showed negative correlations with salinity and the Fmax of fulvic acid-like substances and a positive correlation with the Fmax of protein-like substances. Higher salinity inhibited the tryptophan degradation metabolic pathway and enhanced tryptophan biosynthesis. In addition, higher salinity simultaneously inhibited tyrosine biosynthesis and metabolism pathways. The results of this study may provide a new idea for understanding DOM cycling in brackish lake and organic pollution management.