Hydrogels provide a solution-mimicking environment for the interaction with living systems that make them desirable for various biomedical and technological applications. Because relevant biological processes in living tissues occur at the biomolecular scale, hydrogel nanopatterning can be leveraged to attain enhanced material properties and functionalities. However, the fabrication of high aspect ratio (HAR) nanostructures in hydrogels capable of self-standing in aqueous environments with fine control of the size and shape distribution remains challenging. Here, we report the synthesis of nanostructures with a HAR in bacterial cellulose (BC) hydrogel via directed plasma nanosynthesis using argon ions. The nanostructures in BC are reproducible, stable to sterilization, and liquid immersion. Using surface characterization and semiempirical modeling, we discovered that pattern formation was linked to the formation of graphite-like clusters composed of a mixture of C—C and C═C bonds. Moreover, our model predicts that reactive species at the onset of the argon irradiation accelerate the bond breaking of weak bonds, contributing to the formation of an amorphous carbon layer and nanopattern growth. The mechanical stability of the BC's HAR nanostructures can be potentially used in biosensing and antibiofouling interfaces.