Silver nanoparticles (nAg) are extensively used across various fields and are frequently introduced into aquatic environments, where their behavior depends on environmental conditions. Extracellular polymeric substances (EPS) derived from aquatic organisms, such as diatoms, could play an important yet to be explored role in shaping the fate of nAg in aquatic environments. This study investigates the interactions between EPS, particularly those from the diatom Cyclotella meneghiniana, and citrate-coated nAg. The main objective is to understand how EPS influence the behaviours of nAg in freshwater settings, in terms of modulation of the nAg surface properties, colloidal stability and dissolution. To achieve these objectives a combination of the state-of-the-art spectroscopic and imaging techniques was employed. nAg was incubated with EPS isolated from an axenic C. meneghiniana culture, and their interactions were explored in a simulated freshwater environment over both short-term (0–2 h) and long-term (0–72 h) periods. The study focused on the changes in nAg, examining surface modulation, colloidal stability, dissolution, EPS adsorption on nAg, and the resulting eco-corona formation. The results indicate that EPS enhance the colloidal stability of nAg and decrease their dissolution in synthetic freshwater by adsorbing onto their surface and inducing steric repulsion between nAg particles. Visualization of the eco-corona formed by diatom EPS on nAg and its impact on aggregation processes is achieved through transmission electron microscopy. The formation of the EPS corona is attributed to the presence of diverse biopolymers within EPS, particularly proteins and polysaccharides. Fluorescence quenching studies on protein fluorophores demonstrate the formation, through hydrophobic interactions, of protein–nAg complex, further confirmed by AF4-DAD-FLD-ICP-MS. In a broader context, the results of this mechanistic study imply that diatoms, through the release of EPS, may significantly influence the destiny and possibly the bioavailability of nAg in EPS-abundant aquatic environments.