"The earliest evidence for occupation at Gedi is a grave marker that has been radiocarbon dated to between 1041 to 1278, placing the original settlement of the site sometime in the eleventh or early twelfth century."
In anoher article Wikipedia informs us that it was a harbour:
"Although not thought to be mentioned in historic sources, extensive ruins of a former port have been dated to the thirteenth century or earlier, including a tomb with a date corresponding to 1399, until at least the seventeenth century. Later, the port was abandoned and not rediscovered until the 1920s."
The town was abandoned probably in seventeenth century:
"Gedi's population and prosperity peaked during the fifteenth and into the sixteenth century until it and many other coastal sites began to decline in the late-sixteenth and seventeenth centuries. Gedi was abandoned by the middle of the seventeenth century. "
"Gede’s eventual abandonment to nature is believed to be as a result of a number of factors. Namely, the Wazimba raid along the East African coast in 1589. The removal of the Sheikh of Malindi and the Portuguese to Mombasa in 1593. The falling water table as shown by the deepening of the well outside the Great Mosque and finally the overhanging menace of the Galla, a hostile nomadic ethnic group from Somalia."
Little Ice Age (LIA), climate interval that occurred from the early 14th century through the mid-19th century, when mountain glaciers expanded at several locations, including the European Alps, New Zealand, Alaska, and the southern Andes, and mean annual temperatures across the Northern Hemisphere declined by 0.6 °C (1.1 °F) relative to the average temperature between 1000 and 2000 CE.
Today some scientists use it to distinguish only the period 1500–1850, when mountain glaciers expanded to their greatest extent, but the phrase is more commonly applied to the broader period 1300–1850. "
"The NASA Earth Observatory notes three particularly cold intervals: one beginning about 1650, another about 1770, and the last in 1850, all separated by intervals of slight warming."
I am not saying that it was too cold there and inhabitants escaped from Gede. Simply with rising of continental glaciers the sea level slightly decreased. Today ruins of Gede are around six kilometers from a line of ocean. During the peak of Little Ice Age it was much more and Gede was in the middle of a forest. If the town was the harbour it lost its position. I suppose that if the sea level decreased not so much, people carried goods from ships to town and back but at some moment this activity lost sense and people built new town close to sea line and step by step they moved from Gede to the new location. When the temperature on the world increased and glaciers in Greenland and other places began to melt, the sea level rose again and the water flooded the new settlement. In the meantime, the harbour located in that place have been losing its importance and became depopulated. Maybe Watamu is a remain of that former settlement.
Watching the coast line near Watamu in Google Earth, I started to suppose that maybe the new settlement was established in the current Watamu National Marine Park.
I checked all Kenyan coast line in Google Earth. At the border with Somalia, there is a strange, regular structure in the ocean.