Various methods are employed to investigate the effects of coastal structures in coastal areas on marine environments and transport phenomena. These methods can be categorized into physical models and numerical simulations. Due to the lack of long-term wave height data in Türkiye, numerical models are utilized to estimate wave heights generated by wind based on long-term measured wind speeds. These wave heights generated in deep sea conditions can be transported to the coast by wave transformation and interactions between coastal structures and waves, turbulence, currents induced by wind and breaking waves, coastal sediment transport rates, and changes in the coastline can be successfully predicted with the assistance of numerical models. In the scope of this study, the new “Integrative Probabilistic Design Approach of River Jetties” was developed. 3D numerical models were used for the optimum design, considering the sediment transport near the jetties and aiming to protect the coastal environment in the long term. 3D numerical modeling has been conducted to investigate the transport phenomena occurring at the outlet of the Kabakoz River in the Şile District of İstanbul Province to acquire the optimum layout and design of the coastal structures. The study presents the “Integrative Probabilistic Design Approach” for coastal protection structures by wind and wave climate, wave transformation, coastal sediment transport, shoreline change, and coastal structure probabilistic design sub-models. Monte Carlo Simulation of Hudson Limit State function conducts probabilistic design for the jetties. The greatest advantage of probabilistic design (Monte Carlo Simulation) is the prediction of uncertainties, such as wave height changes under design conditions. Following the completion of the construction of groins, the effect of probabilistic design on both design and coastal morphology can be evaluated precisely. In conclusion, in the study area, 146,237.55 m3 of sediment is transported annually from west to east and 221,043.49 m3 from east to west. In the absence of coastal structures, sediment transport from east to west is approximately 1.5 times greater than from west to east. The annual net coastal sediment transport from east to west is approximately 74,805.94 m3, while the total transport is estimated to be 367,281.04 m3. The coastline is expected to reach sediment balance within approximately two years. In this study, the coastal structure of a jetty is designed from an innovative probabilistic design perspective. The aim is to ensure the reliability of the structure and, at the same time, protect the morphology of the coastline where the structure will be constructed. The region’s wind and wave climate were initially determined using Hydrotam 3D software. Following this procedure, the length of the jetty is predicted considering the closure depth. The model parameters were calibrated from coastline morphology using satellite images and Google Earth over the past twenty years. These parameters are defined to Hydrotam 3D as input data; a trial-and-error model application procedure calibrates the coastline’s accumulation and erosion. Finally, the probabilistic design is conducted with Monte Carlo Simulation using the Hudson Equation as the limit state function. Det Norske Veritas developed a design code for marine structures in 1992, where the target reliability is 10-3 for structures with less serious failure consequences. This reliability level validated the Level IV model presented in this paper. The class of failure depends on the possibility of timely warning, and these standards can be revised by the model presented to address the effects of climate change on the design of maritime structures.