The US President's proclamation came into force as the disaster's death toll rose to 44, after two more fatalities were confirmed in Texas.
Remember, Sunday is National Prayer Day (by Presidential Proclamation)!
— Donald J. Trump (@realDonaldTrump) September 3, 2017
He said: "From the beginning of our Nation, Americans have joined together in prayer during times of great need, to ask for God's blessings and guidance."
The tradition dates back to 1775 when leaders of the Thirteen Colonies called for a day of prayer in their bid to gain independence from Great Britain during the American Revolutionary War.
Mr Trump continued: "As Americans provide much needed relief to the people of Texas and Louisiana, we are reminded of Scripture's promise that 'God is our refuge and strength, a very present help in trouble.'"
"We invite all Americans to join us as we continue to pray for those who have lost family members or friends, and for those who are suffering in this time of crisis."
.@POTUS and @FLOTUS met w/ @uscoastguard heroes in Lake Charles, LA. pic.twitter.com/LvUlbwMNBU
— Sarah Sanders (@PressSec) September 3, 2017
Harvey first made landfall as a Category 4 storm in Texas on 25th August and brought the heaviest tropical downpour ever recorded on the US mainland.
More than one million people have been displaced and tens of thousands of homes have been damaged across the state and neighbouring Louisiana. The cost of damage has run into billions of dollars.
Mr Trump urged Americans "of all faiths" of pray for the bereaved, injured and displaced, as well as police, military and medical staff.
He added: "Each of us, in our own way, may call upon our God for strength and comfort during this difficult time.
"I call on all Americans and houses of worship throughout the Nation to join in one voice of prayer, as we seek to uplift one another and assist those suffering from the consequences of this terrible storm."