Halloysite nanotubes (HNTs)-polyester nanocomposites with four different concentrations were produced using solution casting technique and the biodegradation effect of short-term seawater exposure (120 h) was studied. Monolithic polyester was observed to have the highest seawater absorption with 1.37%. At 0.3 wt % HNTs reinforcement, the seawater absorption dropped significantly to the lowest value of 0.77% due to increase of liquid diffusion path. For samples tested in dry conditions, the Tg, storage modulus, tensile properties and flexural properties were improved. The highest improvement of Tg was from 79.3 to 82.4 °C (increase 3.1 °C) in the case of 0.3 wt % HNTs. This can be associated with the exfoliated HNTs particles, which restrict the mobility of polymer chains and thus raised the Tg. After seawater exposure, the Tg, storage modulus, tensile properties and flexural properties of polyester and its nanocomposites were decreased. The Young’s modulus of 0.3 wt % HNTs-polyester dropped 20% while monolithic polyester dropped up to 24% compared to their values in dry condition. Apart from that, 29% flexural modulus reduction was observed, which was 18% higher than monolithic polyester. In contrast, fracture toughness and surface roughness increased due to plasticization effect. The presence of various microbial communities caused gradual biodegradation on the microstructure of the polyester matrix as also evidently shown by SEM images.