Recently, three-dimensional (3D) city modelling has gained great importance for applications in a wide range of areas including the documentation of city features. During this process, professionals in urban planning, utilities, fire and rescue as well as security turn to GIS data sources. In this study, the Golden Horn (Haliç) is one of the historical and major waterwards located in Istanbul, Turkey which was chosen as the study area due to its unique geographical and historical features. Four models were created with varying levels of detail and discussed in terms of their role in integrated coastal zone management. Coastal areas and estuaries are particularly important sites since they are very sensitive to anthropogenic impact. In this paper, it is also discussed how 3D visual analysis provides scenario-based recommendations to assist urban planners with the decision-making process and creation of new city plans. Besides, a 3D city model for the unique coastal area was modelled and analysed with the help of remote sensing and GIS.