Modification of Java bentonite assists by the multi-step intercalation of sodium and ammonium ions under low-temperature preparation. The adsorbent was examined to remove rhodamine B and methylene blue dyes in an aqueous solvent. The analysis of structural changes conducted by XRD analysis showed the peak shifting from 19.89° to 16.1° and specific peak spectra FTIR of 2846.93 cm-1 due to increase basal spacing from ammonium intercalation. The total capacities of NH-bentonite, Na-bentonite, and Natural Bentonite adsorption to rhodamine B were 192.308 mg/g, 136.936 mg/g, and 116.279 mg/g, respectively, under acidic conditions. Furthermore, the total capacities of NH-bentonite, Na-bentonite, and Natural Bentonite adsorption to methylene blue were 270.27 mg/g, 158.73 mg/g, and 136.986 mg/g, respectively, under alkaline conditions. The adsorption mechanism described that the rhodamine B and methylene blue removal occurred endothermically, was feasible, and adhered to the kinetics model of pseudo-second-order and Langmuir isotherm. It concluded that the modified Java Bentonite from multi-step intercalation is affordable and effective as wastewater treatment.