Clean water is an integral part of industries, agricultural activities and human life, but water contamination by toxic dyes, heavy metals, and oil spills is increasingly serious in the world. Aerogels with unique properties such as highly porous and extremely low density, tunable surface modification, excellent reusability, and thermal stability can contribute to addressing these issues. Thanks to high purity, biocompatibility and biodegradability, bacterial cellulose can be an ideal precursor source to produce aerogels. Here, we review the modification, regeneration, and applications of bacterial cellulose-based aerogels for water treatment. The modification of bacterial cellulose-based aerogels undergoes coating of hydrophobic agents, carbonization, and incorporation with other materials, e.g., ZIF-67, graphene oxide, nanoparticles, polyaniline. We emphasized features of modified aerogels on porosity, hydrophobicity, density, surface chemistry, and regeneration. Although major limits are relevant to the use of toxic coating agents, difficulty in bacterial culture, and production cost, the bacterial cellulose aerogels can obtain high performance for water treatment, particularly, catastrophic oil spills.