Dissolved organic matter (DOM) plays vital roles in carbon and other nutrient transformation at soil-water interfaces (SWI) in paddy fields. It is associated with the growth and withering of periphytic biofilms. However, the interactions between DOM and periphytic biofilms remain largely unknown. In this study, a microcosm experiment with different initial DOM contents elucidated that the biomass, and biomass nitrogen and phosphorus contents were greatly influenced by humic-like substances (C2 and C3), while the growth of periphytic biofilms increased the contents of humic-like (C1 and C2) and tryptophan-like substances (C5) in soil. Moreover, the decomposition of periphytic biofilms significantly increased soil pH, DOM, C2, C3 and C5 contents, but caused decrease in Eh, with consequent reduce in water soluble phosphorus (WSP) and release of algal available phosphorus (AAP). Results from this study revealed how DOM interacts with periphytic biofilms and the consequent effects on changes of bioactive phosphorus fractions, and provide practical information for designing periphytic biofilm based biofertilizer from the perspective of soil DOM.