The biological toxicity and eco-environmental risk of metal nanoparticles (MNPs) is closely related to their stability. The stability of MNPs not only depends on their own properties but also on the effects of biological and environmental factors. To better understand the interaction between biological factors and MNPs in aquatic environments, the effects of total rice root exudates (T-RRE) on the aggregation, dissolution and bioaccumulation of Ag nanoparticles (AgNPs) with different surface charges were investigated in detail. Results indicated that T-RRE can induce the aggregation and sedimentation, and hinder the dissolution of polyethyleneimine-coated AgNPs (AgNPs@PEI) with positive surface charges as well as reducing the bioaccumulation of Ag in rice roots. T-RRE had no obvious effect on the dispersion stability of AgNPs@Cit (negatively charged citrate-coated AgNPs) and AgNPs@PVP (near electrically neutral polyvinylpyrrolidone-coated AgNPs), although T-RRE could induce the dissolution of AgNPs@Cit and AgNPs@PVP. In the molecular fractions of T-RRE, high-molecular-weight root exudates (H-RRE) play a key role in inducing the aggregation of AgNPs@PEI and hindering the bioaccumulation of Ag in rice roots. Compared with H-RRE, low-molecular-weight root exudates (L-RRE) can promote the dissolution of AgNPs@Cit and AgNPs@PVP, but it can obviously promote silver accumulation in rice roots. The difference in charge intensity between L-RRE and T-RRE plays a key role in inducing the aggregation and dissolution of AgNPs with different charges. These findings provide a foundation for investigation of the interactions between rice root exudates and nanoparticles with different surface charges in complex environmental systems.