More than 26 per cent of the island is experiencing a severe drought and another 60 per cent is under a moderate drought, according to the US Drought Monitor.
From 3 July Puerto Rico's utilities company is strictly rationing nearly 140,000 clients water supply and they will be without water for 24 hours every other day.
The company has urged residents not to stockpile water and to maintain social distancing and wear masks if retrieving water from trucks on the island.
“We're asking people to please use moderation,” said Doriel Pagan, executive director of Puerto Rico's Water and Sewer Authority, adding that she could not say how long the rationing measures will last.
Gov Wanda Vazquez confirmed that 21 of 78 municipalities are affected by the severe drought while another 29 by the moderate drought.
Under the administrative order residents in most areas will be prohibited from excessive use of water such as watering gardens during daylight hours, filling pools, and using a hose or non-recycled water to wash cars.
Those who disregard the order face fines from $250 for residents to $2,500 for industries for a first violation.
Gov Vazquez's administration has previously faced criticism for failing to dredge reservoirs to help prevent water loss.
Ms Pagan said that the utility company has been attempting to secure a $300 million dredging investment from the US Federal Emergency Management Agency since hurricane Maria.
She blamed the lengthy process on the number of studies and analysis needed and that require FEMA's approval.
Ongoing dry conditions are set to be interrupted by thunderstorms on Wednesday and Thursday.
“However, we are not expecting enough rain... to solve the problem we're seeing,” Fernanda Ramos, a meteorologist with the US National Weather Service in San Juan said.
The drought comes as the coronavirus pandemic continues to spread across the US and the rest of the world. Puerto Rico has at least 1,630 confirmed cases of the disease and more than 5,600 probable cases. At least 153 people have died on the island due to the novel illness.
The island’s governor extended a coronavirus curfew that began in March for three more weeks to help stem the spread of the virus as it begins to re-open its economy.
“Our priority is to keep our island healthy,” Gov Vázquez said.
The island last endured a drought five years ago which affected 2.5 million people and led to severe water rationing measures causing 400,000 utility customers which meant they received water only every third day.
Additional reporting by the Associated Press.
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