In the present paper, for the first time the ability of the porous biosilica originated from three marine diatom strains of ‘Nanofrustulum spp.’viz.N. wachnickianum(SZCZCH193),N. shiloi(SZCZM1342),N.cf.shiloi(SZCZP1809), to eliminate MB from aqueous solutions was investigated. The highest biomass was achieved under silicate enrichment forN. wachnickianumandN. shiloi(0.98 g L−1DW and 0.93 g L−1DW respectively), and under 15 °C forN. cf.shiloi(2.2 g L−1DW). The siliceous skeletons of the strains were purified with hydrogen peroxide and characterized by SEM, EDS, the N2adsorption/desorption, XRD, TGA, and ATR-FTIR. The porous biosilica (20 mg DW) obtained from the strains i.e. SZCZCH193, SZCZM1342, SZCZP1809, showed efficiency in 77.6%, 96.8%, and 98.1% of 14 mg L−1MB removal under pH 7 for 180 min, and the maximum adsorption capacity was calculated as 8.39, 19.02, and 15.17 mg g−1, respectively. Additionally, it was possible to increase the MB removal efficiency in alkaline (pH = 11) conditions up to 99.08% for SZCZP1809 after 120 min. Modelling revealed that the adsorption of MB follows Pseudo-first order, Bangham’s pore diffusion and Sips isotherm models.