Soil harbors abundant bacteria and viruses that can be delivered into water environments and alter aquatic ecology. However, the mechanisms by which the intruded soil microbes mediate the turnover of dissolved organic matter (DOM) in waters are unknown. Here, we prepared bacterial and phage-enriched inocula from the northern high-humic-composition (NHHS) and southern low-humic-composition (SLHS) soils in China, and investigated their roles in aquatic DOM transformation via microcosm experiments. The aquatic DOM was more rapidly degraded by the soil-derived microbes than the aquatic microbes. However, associated with the soil regions, phage-enriched inocula caused two different molecular transformation patterns. Unlike the NHHS soils, phage-enriched fractions from the SLHS soils can enhance the bacterial decomposition of DOM (especially many aromatic CHO and S-containing compounds), while inhibiting the accumulation of few aliphatic molecules with O/C < 0.5 and H/C > 1. Additionally, the potential effects of soil virus-enriched fractions on the microbial degradation of aquatic DOM can be largely predicted by the organic composition in soils. Our findings demonstrate the divergent and environment-associated roles of different soil microbial fractions in aquatic carbon cycling, which provide new insights into the biogeochemical consequences of soil microbiome transfer in the land-water continuum.