The silica particle interactions in the presence of spermidine were systematically investigated both from experimental and theoretical points of view. The hydrodynamic radii and the corresponding polydispersity indices of the colloidal silica particles were determined by dynamic light scattering (DLS) as a function of spermidine concentration. Whereas the effective size of the silica particles increases with increasing spermidine concentration (pointing to the particle aggregation), the polydispersity index first increases reaches a maximum and then further decreases with the increasing spermidine concentration. From the mobility measurements it was concluded that the increase in spermidine concentration causes less negative values of zeta potential, meaning that the adsorption of spermidine leads to the less negative silica surface. Moreover, Monte Carlo (MC) simulations also confirmed that the addition of spermidine reduces the repulsion between silica particles. The MC concentration profiles of spermidine close to the charged silica particle are in a very good agreement with the results obtained by theory. An important motivation for our study is the effectiveness of multivalent ions to coagulate colloidal suspensions; e.g., the multivalent ions are exploited in the water purification process.