<p>Pile-raft foundations, as hybrid structural systems, are increasingly adopted to support the substantial and complex loads imposed by high-rise and industrial structures. This study presents a comprehensive three-dimensional finite element analysis to investigate the load intensity–settlement behavior of pile-raft foundations in clayey soil deposits, with emphasis on the influence of seasonal groundwater table fluctuations. The analysis incorporates raft-to-pile, pile-to-pile, pile-to-soil, and raft-to-soil interactions to capture the coupled response of the system. Key parameters examined include raft thickness (<i>t</i>_<i>r</i>), pile spacing-to-diameter ratio (<i>s/d</i>), pile-diameter (<i>d</i>), pile length-to-diameter ratio (<i>l/d</i>), soil cohesion (<i>c</i>) and pile number (<i>N</i>). Results show that increasing pile diameter, pile length, pile number, and soil cohesion significantly enhances the ultimate load-bearing capacity (ULC) and reduces settlement, with settlement reductions of up to 48% and 62% for longer piles and higher cohesion, respectively. Conversely, larger raft thickness, higher <i>s/d</i> ratios, and a shallower groundwater table amplify settlement, with a maximum settlement value of 1.31&#xa0;m for a 2&#xa0;m thick raft. Seasonal groundwater variations notably impact foundation performance. When the water table is at the pile head, settlement increases by up to 29% compared to deeper water table positions, primarily due to reduced effective stress. Beyond 15&#xa0;m depth, the groundwater position shows a negligible effect. The study recommends adopting higher pile group configurations in regions with fluctuating groundwater levels to minimize excess settlement and enhance load-bearing efficiency.</p>