The sustainability of high-level radioactive waste repositories situated in fractured crystalline rocks depends on the stability of bentonite liners, and this can pose a problem in certain groundwater conditions that favor the formation of colloids from backfill materials that are prone to erosion. The influence of different environments on the structure of Gaomiaozi bentonite (GMZ) and GMZ colloids (GMZC) is presented here. Different hydrated interlayer structures of bulk and colloidal forms of this bentonite from small-angle X-ray scattering (SAXS) data are demonstrated. Analysis of the scattering data showed that GMZ had three interlayer water structures: dehydrated (0W), monohydrated (1W), and bi-hydrated (2W). The colloids readily agglomerated at acidic pH (pH <5) but showed resistance to agglomeration in an alkaline condition (pH >7). The effect of Na+, K+, Mg2+, and Ca2+ on the lamellar structure and agglomerate morphology of GMZC particles was investigated. In general, the tendency of colloids to agglomerate was greater in the presence of divalent metal cations compared with monovalent metal cations. High concentrations (10–5 to 10–3 mol L–1) of divalent ions imparted order into the stacked lamellar structure after the saturation of the interlayer. In contrast, monovalent ions reduced the tendency of the particles to aggregate, leading to an abundance of colloidal nanoparticles prone to erosion. This work helps to better understand the structural characteristics of GMZC in the groundwater environment, and provides a valuable reference for the evaluation of nuclide migration in the deep geological disposal of high-level radioactive wastes.