This study performs a bow-tie analysis concerning biodiversity change in the Broad Belt Transect of Heraklion Bay (BBT12) in the framework of MARBEFES project. Heraklion Bay is currently undergoing changes mostly due to climate change, tourism and urbanisation. This affects the marine environment via marine heat waves, mass mortality events and tropicalisation. Introduction of invasive species is on the rise in the area and together with the transformation of typical Mediterranean rocky reefs to barren reefs is leading to an ecosystem shift and significant changes in biodiversity. In addition, tropicalisation can also be linked to the reduction of marine biological resources affecting the local fisheries. Furthermore, recent studies of macrobenthic communities of soft-bottom habitats in the area contribute to understanding the spatial and temporal trends and changes in biodiversity due to multiple environmental and human-induced disturbances. These changes reduce the ecosystemic resilience and can affect ecosystem services we take for granted. Within the framework of the project, stakeholders of Heraklion BBT have been surveyed and interviewed and their views concerning balance between nature, society and economy have also been incorporated into the bow-tie analysis. Their main concern for Heraklion BBT is the extensive development of large-scale tourism in the area. All these pressures have negative effects on the marine environment of the area and socio-economic impacts on the population of the area. Having this in mind, prevention and mitigation measures are presented.