In view of a great demand for paper-based technologies, nonwettable fibrous substrates with excellent durability have drawn much attention in recent years. In this context, the use of cellulose nanofibers (CNFs), the smallest unit of cellulosic substrates (5-20 nm wide and 500 nm to several microns in length), to design waterproof paper can be an economical and smart approach. In this study, an eco-friendly and facile methodology to develop a multifunctional waterproof paper via the fabrication of fluoroalkyl functionalized CNFs in the aqueous medium is presented. This strategy avoids the need for organic solvents, thereby minimizing cost as well as reducing safety and environmental concerns. Besides, it widens the applicability of such materials as nanocellulose-based aqueous coatings on hard and soft substrates including paper, in large areas. Water droplets showed a contact angle of 160° (±2°) over these surfaces and rolled off easily. While native CNFs are extremely hydrophilic and can be dispersed in water easily, these waterborne fluorinated CNFs allow the fabrication of a superhydrophobic film that does not redisperse upon submersion in water. Incorporated chemical functionalities provide excellent durability toward mechanochemical damages of relevance to daily use such as knife scratch, sand abrasion, spillage of organic solvents, etc. Mechanical flexibility of the chemically modified CNF composed paper remains intact despite its enhanced mechanical strength, without additives. Superhydrophobicity induced excellent microbial resistance of the waterproof paper which expands its utility in various paper-based technologies. This includes waterproof electronics, currency, books, etc., where the integrity of the fibers, as demonstrated here, is a much-needed criterion. © 2017 American Chemical Society.