Adhesively bonded hybrid FRP-aluminium structures have recently become an efficient solution for marine engineering applications. However, polymer adhesives' bond performance is sensitive to the marine environment due to polymer and interfacial degradation. This study aims to develop mode I, mode II delamination toughness, and Tg data as a comprehensive design guideline for hybrid BFRP-aluminum modified-adhesively bonded joints subjected to seawater aging. The hybrid joints were exposed to long-term seawater aging (for 6 months) to reveal their fracture and thermomechanical performances. Besides, the adhesive was reinforced with HNTs to increase fracture resistance with additional nano-scale toughening mechanisms and to delay the water absorption. After the long-term aging, reinforced adhesively bonded joints exhibited ∼36% higher fracture toughness than neat adhesively bonded joints. Moreover, DMA was conducted on miniaturized SLJ samples, which revealed that HNT modified adhesive joints showed ∼11.5 °C higher Tg. The calculated aging rates also proved the effectiveness of HNTs modification on the epoxy adhesive's aging performance since the HNT reinforced adhesive represented 43% lower aging rates in terms of storage modulus. It is considered that experimental results will help comprehend long-term aging influences on the composite-aluminum hybrid designs’ fracture and thermomechanical performances. These exciting findings will pave the way for the safe use of high stiffness and cost-effective aluminum-BFRP hybrid structures for the marine industry.