Stone boulders breakwaters are the most widespread and widely used type of breakwaters. if the foundations of these structures do not have sufficient bearing capacity, large settlements will await the structure. Since the construction of these projects is expensive, and the supply of suitable stone resources are essential for the construction of these projects, a relatively good prediction of the stone materials volume used in the project is important. Therefore, a research project was carried out at Siyadi Port breakwater, (Iran) utilizing geotechnical data and construction observations. The objective was to create a computer model to understand the response of the clay bed to the weight of the rocks. This analysis was done by Lagrangian equations and using FLAC software and led to the selection of characteristic of soil parameters that simulated the subsidence of materials on an elasto-plastic bed. Soil resistance parameters that could not be determined through standard tests were derived through a process of back analysis. The study also investigated the effects of the thickness of the loose layer, variations in sea water levels, and the use of geotextile in the project. A large rise in settling is anticipated as the muddy soil's depth increases. Results also confirms the effectiveness of using geotextiles for settlement management. Moreover, updated characteristics of soil from the previous step in order to comprehend the construction of an entire breakwater section on muddy soil seems crucial. With this method, long-term settlements and the stability of the breakwater section may be reliably predicted.