In the last 100 years, the population of the land of Israel has increased dramatically, accompanied by a very intense and accelerated economic and industrial growth. The objective of the present review is to reveal how these major changes have affected the Mediterranean marine and coastal environment. The present review analyzes the global, regional, and local factors and processes that cause substantial environmental changes affecting a variety of marine habitats and taxa. These include: (1) seawater warming that enhances the considerable introduction and establishment of non-indigenous tropical, i.e., Lessepsian, species; (2) overfishing of native biota that seems to contribute to this process; (3) sea-level rise, associated with global warming, which may threaten the sensitive intertidal abrasion platforms; (4) chemical, noise, and light pollution and marine debris; (5) massive sand mining from the beaches, which caused severe erosion in many coastal sections and was banned in Israel in 1964; (6) extensive dredging in the sea, mainly related to the construction and development of large ports, which can be detrimental for the benthic biota, especially in rocky substrates; and (7) marine structures (harbors, marinas, detached breakwaters) that interfere with the natural pattern of sand transport along the coast and cause morphological changes (sand erosion or accumulation) on nearby beaches and the seabed. Israel’s coast is presently characterized by intense anthropogenic activity and many stakeholders with considerable conflicts between them and with the marine ecosystem. A few environmental impacts have ceased, and others have been reduced considerably, but the extent of many additional types have increased significantly, and new impacts have appeared in recent years. Some environmental impacts are beyond our control, and others can be reduced by proper management, but it is predicted that certain major environmental impacts, such as Lessepsian migration, will continue in the future at enhanced rates.