Polonnaruwa went to decline, civil war, lawlessness and constant invasions from the South Indian Chola Empire, and Malay barbarians who sacked the city several times, virtually destroyed the social structure and religious order of the country. A whole century after this were the 'Dark Ages' of Sri Lanka, a century from which few historical records survive.

The capital was shifted to Kurunegala, and Polonnaruwa returned to the jungle; it's great reservoirs survived as a series of swampy lakes, and its large brick buildings became lost under thick tropical forest. The Portuguese are said to have raided and looted Polonnaruwa, but by the early nineteenth century the site was completely lost.

In the early years of this century the main monuments of the ancient city were uncovered. Today, conservation and excavations continue, as part of the work of the Cultural Triangle.