The severe weather also knocked over several trees and forced authorities to close various main roads, with more than a dozen people remaining in shelters after their homes flooded.
Up to six inches of rain fell in less than six hours in some places, said Nino Correa, commissioner for the Bureau of Emergency Management and Disaster Administration.
Toa Alta, a town in Puerto Rico's northern region, received the most rain with nearly 16 inches over the weekend, according to the National Weather Service in San Juan.
Flooding along coastal areas was worsened by large waves of up to 13 feet hitting the island's north coast on Saturday and Sunday.
Source: AP
A look at wind movement at 700hpa shows a steady airstream rising from the equator travelling south of the island before it heads North East up the Eastern side of the USA. Now under normal circumstances that wouldn't be a problem but for a small matter of cold air cascading it's way down through the Atlantic ocean and heading West towards Puerto Rico at 500hpa.
The net result is the formation of a loop of precipitable water within the atmosphere that is the cause of said rainfall.
Outlook, further heavy rainfall is to be expected.