An elongated region of sandstone reefs acted as a 6-kilometre natural breakwater in the area 8,000 years ago. By 6,000 years ago, rises in sea level had reduced the length of the island from 6 to 4 kilometres. This, combined with an increase of sediment supply due to agricultural activity and a rise in inland rainfall, particularly after about 3,000 years ago, created a natural sandbar that sat an average of 1-2 metres below mean sea level in Alexander's time, they report in Proceedings of the National Academy of Sciences1
So, there was a natural sandstone at some location (not shown?) that had been increasing sedimentation between the island and mainland, increasing after 3k BP. Thus, Alexander only had to build in 2-3m of water.