The evolution of highly efficient adsorbents has received attention around the world due to the importance of removing pollution from water. In the current work, a new and stable silica/coordination polymer nanoporous composite was prepared via the layer-by-layer method and characterized with various physicochemical methods. Aminopropyl-functionalized SiO2 was consecutively coated with Ni2+ and glutaric acid (GA) in 10 steps to prepare SiO2/Ni-GA. The removal efficiency of SiO2-based nanoporous composite towards cationic and anionic dyes was considered at room temperature. The results showed that SiO2/Ni-GA is a good adsorbent for all selected dyes (Congo red, CR; methyl orange, MO; and malachite green, MG). However, CR with higher removal efficiency (94%) was selected for further investigations. The high removal efficiency of SiO2/Ni-GA towards CR is related to hydrogen bonding and relatively good surface area. The adsorption process was well fitted with the second-order kinetic model and the recovered adsorbent was shown to be reusable for three consecutive cycles.