Bacterial cellulose (BC)/Fe3O4 aerogels were fabricated by a simple immersion of BC hydrogels in commercially available ferrofluid solution followed by freeze-drying. The BC/Fe3O4 aerogels were converted into carbon nanofiber (CNF)/Fe3O4 aerogels by pyrolysis at 600 °C. With our fabrication methods, the Fe3O4 nanoparticles (NPs) were effectively impregnated and homogeneously distributed in the nanostructures of BC and CNF. The average diameters of the BC and CNF nanofibers were found to be about 79.3 ± 14.1 nm and 56.7 ± 13.6 nm, respectively. Increasing the ferrofluid concentration resulted in a nonlinear increase of Fe3O4 NPs loaded into the BC and CNF structure, but the functional groups were not affected. The saturation magnetization (Ms) of CNF/Fe3O4 was larger than those of BC/Fe3O4 and increased with the amount of impregnated Fe3O4 NPs. The maximum magnetization in our work was larger than literature values, with the highest Ms of 82.9 emu/g approaching the bulk value of Fe3O4. The materials presented could be used as pollutant absorbers for wastewater treatment. We have demonstrated the capability of using magnetic CNF aerogels in absorbing a common dye pollutant from water. The dye was absorbed efficiently, and the aerogels were easily magnetically removed from the solution and are reusable.