Hydrothermal conversion plays a crucial role in efficiently converting biomass s. There are organic acids and active compounds in aqueous phase product: Under certain reaction temperature and pressure hydrothermal treatment, biomass undergoes degradation and polymerization, yielding valuable small molecular acids and macromolecule humic acid, and other active compounds. The feedstock species and operational conditions influenced the yield and compounds distribution of hydrothermal aqueous products. These compounds showed various application potential including phytopathogen control, advanced material preparation, energy output and soil fertilizer, fostering comprehensive biomass utilization. Considering the effect of antimicroorganism and soil improvement of aqueous phase, the organic and inorganic compounds can be cyclically utilized in agriculture, serving as biofertilizers, soil amendments and phytopathogen control agents. In this chapter, the influence of compositions in feedstocks and operational conditions on organic acids and antimicrobial compounds in aqueous phase were discussed. Furthermore, the chapter addressed the potential application of hydrothermal aqueous product in agriculture for phytopathogen control and soil fertilizer. However, the challenge of agricultural application lies in the uncertainties of the beneficial components, environmental safety and crop safety.