Although structural polymers like epoxy are extensively used in marine applications over metallic structures, environmental water tends to ingress into this polymer which may affect its long-term durability. The extent of degradation caused by the absorbed water on polymeric composite's mechanical properties depends on the water diffusion mechanism, environmental temperature and subsequent reversible and irreversible chemical restructuring of the polymer. In this study, hydrothermal conditioning behavior of glass fiber reinforced epoxy (GE) composites with varying (0.1, 0.3, and 0.5) wt.% of pristine and functionalized carbon nanotubes (CNTs and FCNTs) was studied at 15°C (Low-Temperature Hydrothermal Conditioning (LTHC)) and 50°C (Elevated-Temperature Hydrothermal Conditioning (ETHC)) water baths. The changes in chemical bonding characteristics and glass transition temperature of GE composite due to above mentioned factors have been studied by Fourier transformed infrared spectroscopy and differential scanning calorimetry. The gravimetric analysis was employed to monitor the water uptake kinetics of the composites and flexural strength of conditioned composites after 50 days of conditioning and saturation was study to understand the effect of water sorption. Experimental results revealed that, FCNTs greatly hinders the water absorption through the interfaces at LTHC, as the equilibrium water content of 0.1FCNT-GE composite was ~9.5% and ~3.0% and Diffusion coefficient was ~60.0% and ~15.5% lower than the GE and 0.1CNT-GE composites, respectively at LTHC. At LTHC, the water saturated 0.1FCNT-GE composites exhibited superior flexural strength than GE and 0.1CNT-GE composites. At ETHC, generation of hygroscopic stresses and unfavorable stresses at the weak CNT/polymer interface adversely affected the 0.1CNT-GE composites water resistance compared to 0.1FCNT-GE composites with stronger FCNT/polymer interface. The extent of recovery in the flexural strength was evaluated by complete desorption of water-saturated specimens. Finally, a fractography study was conducted to understand the variation in the well-being of the glass fiber/polymer and nanotube/polymer interface due to mentioned varying factors.