This study investigates the influence of thermoplastic polyurethane (TPU) reinforced with jute cellulose nanofibers (CNFs) on the water absorption and mechanical properties of geopolymer concrete. The integration of TPU/jute CNF nanocomposites into geopolymer concrete is explored as a strategy to enhance both its durability and mechanical performance. Geopolymer concrete, a sustainable alternative to traditional Portland cement concrete, is known for its low carbon footprint, but it suffers from high brittleness and water absorption. The water absorption behavior of the modified concrete was assessed, revealing a significant reduction in water uptake due to the hydrophobic nature of TPU and the reinforcing effect of jute CNFs. Additionally, the mechanical properties, including compressive and flexural strengths, were evaluated to understand the impact of the nanocomposites on the structural integrity of the concrete. The addition of TPU/jute CNFs notably enhanced the splitting tensile strength (63.5%), compressive strength (59%), and water absorption (0.59%) of the composite, indicating a promising route for developing high-performance construction materials. The integration of 6 wt% of TPU/jute CNF nanocomposites was found to be optimal, resulting in a uniform matrix, reduced micro-cracks, and improved compressive strength due to enhanced adhesion between the nanocomposites and the geopolymer matrix. Furthermore, a curing temperature of 100 °C was identified as ideal, minimizing unreacted fly ash and enhancing adhesion strength, while higher temperatures (140 °C) led to material deterioration due to rapid water loss. The findings demonstrate that the addition of TPU/jute CNF nanocomposites not only improves resistance to water penetration but also enhances overall mechanical performance. This supports the development of more sustainable and resilient construction materials, contributing to global efforts to reduce the environmental impact of the construction industry. Future research should focus on the long-term durability of these composites under various environmental conditions to validate their effectiveness in real-world applications.