Na-magadiite materials were prepared from a gel containing a silica source, sodium hydroxide, and water via hydrothermal treatment at different temperatures (130 ◦C to 170 ◦C) and periods of time (1 day to 10 days). In this study, four silica sources were selected (fumed silica, colloidal silica, Ludox HS-40%, and Ludox AS-40%). Variable conditions such as sodium hydroxide and water contents were explored at a specific temperature and reaction time. The obtained materials were characterized by using X-ray diffraction (XRD), thermogravimetry differential thermal analysis TG-DTA, scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX), Fourier Transform Infrared spectroscopy (FTIR), solid 29Si magic angle spinning magnetic nuclear resonance (MAS MNR, and nitrogen adsorption isotherms. A pure Na-magadiite phase was obtained from the four silica sources at a synthesis temperature of 150 ◦C after a period of one to two days with a characteristic basal spacing of 1.54 nm. At a longer reaction time of 3 days and a higher temperature of 170 ◦C, Na-kenyaite with a basal spacing of 2.01 nm was achieved, in addition to a quartz phase. The content of water or sodium hydroxide in the gel affected the nature of the prepared phases. A cauliflower-like morphology was obtained from colloidal silica sources, while a different morphology was achieved using solid fumed silica. The 29Si solid NMR confirmed the presence of Q3 and Q4 silicon sites in the Na-magadiite materials. The optimal Na-magadiite materials at 150 ◦C for 2 days were assessed for their ability to remove Basic Blue-41 dye from artificially contaminated aqueous solution. The Langmuir equation was used to estimate the maximum removal capacity. A maximum removal capacity of 219 mg/g was achieved using Na-magadiite prepared from a Ludox-HS40% silica source, and a maximum removal capacity of 167 mg/g was observed for Na-magadiite prepared from fumed silica. Basic Blue-4’s removal percentage was enhanced at basic pH levels (8 to 10) to a maximum of 95%. These materials could be regenerated for seven cycles of reuse with a reduction of 27 to 40% of the original values. Therefore, Na-magadiite materials are promising and efficient removal agents for the removal of Basic Blue-41 from effluents.