The aggregation kinetics of negatively charged borate-stabilized silver nanoparticles (NPs) induced by the cationic regioregular polythiophene polyelectrolyte poly{3-[6-(1-methylimidazolium-3-yl)hexyl]thiophene-2,5-diyl bromide} (PMHT-Br) and the morphology of formed aggregates have been investigated via ultraviolet-visible light (UV-vis) spectroscopy, transmission electron microscopy (TEM), zeta (ζ) potential measurements, dynamic light scattering (DLS), and time-resolved small-angle X-ray scattering (SAXS). Two or three populations of NPs are formed within milliseconds upon mixing the components, which differ in the mean size, extent of polymer coating, and time stability. These characteristics are primarily controlled by the PMHT-Br to Ag-NPs ratio. Population of single NPs of a mean size of ∼5 nm is present in every system and is mostly stable for a long time. At low ratios, the single NPs are most probably almost free of polymer chains and the second population includes slow, but in a limited extent, growing NPs in which single NPs might be interconnected by polymer chains. At the ratios corresponding to the charge balance in the system (ca. zero ζ-potential of NPs), the NPs aggregate, forming a second population that continuously grows in size, and finally undergo sedimentation. At the high ratios, three long-time stable populations of NPs are observed, having mean sizes of ca. 5, 13, and 35 nm; all NPs should be fully coated with PMHT-Br, giving them a positively charged stabilizing shell.