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Green and biodegradable materials are also being considered as an alternative to the plastic-based products in the textile and packaging sectors as a sustainable alternative. In this study, four kinds of jute-based fabrics were used that included raw jute woven, bleached raw jute woven, jute-cotton union and bleached jute-cotton union subjected to a dip-pad-dry-cure to acquire water-repellent properties with the usage of Rucostar EEE6 (a C6-Fluorocarbon resin containing hyperbranched polymers in a hydrocarbon matrix). In the presence of acetic acid, finishing solutions of different concentrations of Rucostar EEE6 (120, 140 and 160 g/L) were prepared. Treated fabrics were dried at 100 °C at 30 mins and cured at 160 °C for 1 min to enhance fixation. Structural, chemical, mechanical, and functional characterizations were systematically performed to evaluate the performance of the treated fabrics. The use of Scanning Electron Microscopy (SEM) showed a consistent deposition of the finishing layer on the fiber surface and Fourier Transform Infrared (FTIR) spectroscopy showed that the resin chemically reacted with the hydroxyl groups of the jute cellulose. Tensile strength test was performed in order to determine the impact of finishing on the durability of fabrics. Contact angle, spray rating test (AATCC Method 22) and drop test were used to assess water-repelling performance. The contact angle of the treated fabric was more than 90, which confirms that the fabric is hydrophobic. It is important to note that the sample treated with 140 g/L of Rucostar EEE6 and cured at 160 °C had a spray rating value of 100, which means the highest water repellency level and a high degree of water penetration resistance. On the whole, the results indicate that jute fabric with fluorocarbon resin finish exhibits a considerable improvement in hydrophobic properties and retains mechanical strength and natural feel, which implies a high level of potential application in the sustainable development of the textile industry as an alternative to plastic bags.