<p>Sea-crossing, long-span, and cable-stay bridges are essential elements of transportation networks in coastal regions and significantly contribute to the advancement of regional economies. Sea-crossing cable-stay bridges may face a confluence of severe natural hazards, including seabed earthquakes, wind-generated waves, and currents, which can significantly jeopardize their operational safety. Furthermore, the intricate coastal environment subject’s offshore railway bridges to substantial reactions when vehicles cross these maritime structures. It is essential to assess the modal properties of the bridge before performing a dynamic analysis of its structure, which is vital. The vibrational frequencies of the SCB bridge system impact multiple simulated modes; hence, enhancing bridge analysis and design through precise calibration of eigenfrequencies via mass and stiffness distribution is essential to prevent resonance and retain structural integrity, safety, and functionality. Further investigation is required about the modal characteristics of long-span SCB for vibration investigation and control. However, there is limited literature regarding the modal properties of long-span SCB. The primary aim of the present research is to develop a computational representation of an SCB cable-stayed system and analyze how different parameters affect its modal characteristics, namely its inherent frequencies and associated mode configurations. Additionally, it examines the impact of variations in modal parameters on an SCB across water and soil using a computational model for an SCB that incorporates fluid-structure interaction (FSI) and structural interaction (SSI) effects. The current study constructed a comprehensive 3D FEM simulation for an SCB over a body of water and compared its natural frequencies with those found in previous studies. The simulation's validity was validated through a mesh convergence investigation and compared with findings from earlier studies. This work analyses the modal response simulation of a cross-sea bridge featuring twin H-shaped pylons and a rectangular pier. The present study performed a modal analysis of the SCB, using both SSI and FSI, to determine the frequencies and mode shapes of the SCB. Subsequently, the exploration of the structure's inherent vibration frequency investigates the influence of the correlation between water-structure and soil-structure rigidity on the structure's natural vibration frequency. The consideration of this study's cumulative mass participation factor indicates that the SCB system accounts for 90% of the overall mass in the initial 10 phases. The results reveal that SSI reduces the natural frequency of SCB due to increased mass impact when compared to the non-SSI scenario. Nonetheless, soil stiffness may affect frequency changes. The dirt around the bridge foundation could potentially add mass to the system. The extra mass frequently lowers natural frequencies. The rigidity of the soil can affect the overall rigidity of the bridge-soil framework. Reduced soil rigidity may cause reduced system stiffness and lower natural frequencies. Stiffer soil can stiffen the system and increase natural frequencies. FSI has frequently resulted in lower predicted natural frequencies when compared to the "no FSI" case. The nearby water adds heft to the bridge framework. The extra mass frequently lowers natural frequencies. Water exerts drag forces on the bridge, generating damping that can somewhat alter natural frequencies but primarily impacts the rate of vibration decay. Interaction with water can change the adequate rigidity of the bridge structure, hence influencing its natural frequencies. Increased frequencies occur when accounting for a higher grade of concrete. The present study emphasizes the modal evaluation of a SCB structure. Bridge and railway engineers can leverage this investigation to enhance the structural efficiency and functionality of the SCB. Moreover, it may serve as a basis for subsequent assessments of dynamics and fatigue, considering the numerous dynamic loads that impact the SCB.</p>