To gain important information on fate, mobility, and bioavailability of silver nanoparticles (AgNP) in aquatic systems, the influence of pH, ionic strength, and humic substances on the stability of carbonate-coated AgNP (average diameter 29 nm) was systematically investigated in 10 mM carbonate and 10 mM MOPS buffer, and in filtered natural freshwater. Changes in the physicochemical properties of AgNP were measured using nanoparticle tracking analysis, dynamic light scattering, and ultraviolet–visible spectroscopy. According to the pH-dependent carbonate speciation, below pH 4 the negatively charged surface of AgNP became positive and increased agglomeration was observed. Electrolyte concentrations above 2 mM Ca²⁺ and 100 mM Na⁺ enhanced AgNP agglomeration in the synthetic media. In the considered concentration range of humic substances, no relevant changes in the AgNP agglomeration state were measured. Agglomeration of AgNP exposed in filtered natural freshwater was observed to be primarily controlled by the electrolyte type and concentration. Moreover, agglomerated AgNP were still detected after 7 days of exposure. Consequently, slow sedimentation and high mobility of agglomerated AgNP could be expected under the considered natural conditions. A critical evaluation of the different methods used is presented as well.