A general solution-phase strategy is developed to synthesize nanostructure niobates such as MnNb 2 O 6 , SnNb 2 O 6 and ZnNb 2 O 6 on natural mineral diatomite for water environmental remediation. (NH 4 ) 2 C 2 O 4 aqueous solution is the key to achieve a scalable and controllable synthesis of niobate/diatomite hybrid systems, which generates NH 3 $H 2 O for surface etching activation of diatomite, and H 2 C 2 O 4 for complexation dissolution of Nb 2 O 5 , enabling the heterogeneous crystallization process to proceed with controllable growth kinetics. First principle calculations indicate that both niobium atom and niobiumoxygen species have the lowest adsorption energy on SiO 2 surface, and then induce the nucleating process of Nb-O-Mn (or Zn, Sn) networks. Cr(VI), Fe(III), and Pb(II) ions are taken as target pollutants to evaluate the water-cleaning ability of the niobate-modified diatomite. Possible mechanisms for the photoreduction of Cr(VI), physical adsorption of Fe(OH) 3 colloids, and chemisorption of Pb(II) ions are proposed on the basis of experimentally investigations. The possibility of combining the advantages of natural mineral diatomite and nanostructured niobates provides a highly robust and potential material system with versatile functionalities of heavy metal ion removal, demonstrating great promise for a wide range of water purification.