A series of SBA materials (SBA-12, SBA-15, and SBA-16) with polyethyleneimine (PEI) and its Schiff base variants with salicylaldehyde-modified samples (PS) have been successfully prepared and characterized. The synthesized materials were investigated by infrared spectroscopy (FT-IR), and quantification of the organic part coated on the surface was studied using thermogravimetric analysis (TGA). Nitrogen adsorption/desorption analysis at − 196 °C (N2), bright field scanning transmission electron microscopy (BF-STEM) and small angle X-ray scattering (SAXS) measurements were used to study textural properties, structure and morphology. Confirmation of heavy metal ions capture in pores of prepared materials was proved by X-ray fluorescence analysis (XRF), and nitrate anions were confirmed by FT-IR spectroscopy. Kinetic studies were performed by conductometric analysis (CA) and showed that the mathematical models could be applied to adsorption processes with a non-linear decreasing trend. This trend appeared in PS-modified SBA systems and some non-modified samples. The best overall adsorption properties were observed for material SBA-12 and its modified types. In this case, material SBA-12-PS can trap 54.38 mg g−1 of Cu(NO3)2 or 18.42 mg of Cu(II) ions, 112.84 mg g−1 of Ni(NO3)2 corresponding to 36.24 mg of Ni(II) cations, and 39.56 mg g−1 of Co(NO3)2 representing 12.74 mg of Co(II) ions. Non-modified materials show morphological effects where 2D ordered pores with hexagonal symmetry and the biggest mesopores (5.5 nm) have the best overall results in adsorption capacity of metal ions (Cu(II): 11.95 mg g−1) calculated from pseudo-second order. SBA-12 with a cubic framework and 3D ordered pores (3.8 nm) has a lower adsorption capacity than SBA-15 (Cu(II): 7.85 mg g−1), and SBA-16 with the smallest spherical pores (under 2 nm) showed the lowest overall adsorption capacity (Cu(II): 4.65 mg g−1). Kinetic rates of non-modified samples have opposite trend SBA-12 (Cu(II): 0.009 mg g−1 min−1) > SBA-15 (Cu(II): 0.002 mg g−1 min−1) > SBA-16 (Cu(II): 0.001 mg g−1 min−1). In the case of SBA-16, small pore entrances have a negative effect on the kinetic rate. For modified samples, SBA-12 with the largest surface area (896 m2 g−1) provides more space for binding of polyethyleneimine molecules (and also salicylaldehyde), which affects the best results in ion capture (Cu(II): 16.64 mg g−1). Bigger mesopores give more adsorption capacity, but capillarity makes the kinetic rate slow. SBA-16, with tiny entrance mesopores, has the lowest kinetic rate and adsorption capacity. This phenomenon was also observed in cobalt(II) adsorption, and similar results were obtained in nickel(II) adsorption. Kinetic studies point to two types of mechanisms given by the pseudo-second-order model in the case of non-modified materials, and Elovich kinetic model describes chemisorption at modified samples. These mechanisms are influenced by the significant effect of intraparticle diffusion, described by the Weber-Morris model.