Although he signed the bill, the president called it "seriously flawed" and said it "improperly encroaches on executive power, disadvantages American companies, and hurts the interests of our European allies".
Russian Federation responded by saying the sanctions amounted to a full-scale trade war and an end to hopes for better ties with the Trump administration.
Russian Prime Minister Dmitry Medvedev has penned a scathing Facebook post in response to new USA sanctions, decrying what he described as the Trump administration's "total weakness" and saying that the package "ends hopes for improving our relations with the new administration".
Though that language may strike some as harsh, legal and political experts say it isn't uncommon or out of line with what presidents in recent history have done when it comes to commenting on legislation they are signing into law.
He added: "The President is not happy about the sanctions, yet he could not but sign the bill".
Moscow, which announced a series of retaliatory measures over the weekend, has painted the bill's passage in the Senate as a humiliation for Mr Trump.
The White House said only that Trump would give Congress's "preferences" mere "careful and respectful consideration".
The Foreign Ministry emphasized that "we naturally reserve the right for other countermeasures".
Sen. Charles E. Schumer of NY, the top Democrat in the Senate, took his own shot on Twitter, calling the bill "a model for the future" that shows both parties can work together "to rein in" Trump "when he veers off track".
One of Trump's frequent critics, Republican Senator John McCain, laid the blame for the deteriorating U.S. -Russia relationship on Putin.
The decision of downsizing has caused major discomfort in Washington, as well as concerned US officials who are now present in Moscow.
He said Russian Federation would cope with the challenge and only get stronger, but warned it had ended "hopes for improving our relations with the new USA administration".
"I love the White House, one of the most handsome buildings (homes) I have ever seen", Trump said.
He signed it without holding a public event. The new measure targets Russia's energy sector as part of legislation that prevents Trump from easing sanctions on Moscow without congressional approval.
In a fresh outburst on Thursday, he made clear who he thought was responsible for the current state of US-Russia ties.
A special prosecutor is investigating whether Mr Trump advisers colluded with what USA intelligence has concluded was an attempt by Russian Federation to covertly support the real estate mogul's 2016 campaign.
Russia's government responded to the sanctions by ordering the USA embassy and missions in Russian Federation to reduce its diplomatic staff.
The sanctions are related in part to findings by the intelligence community that Russian Federation interfered in the USA presidential election through a coordinated effort that included hacks of political organizations and a promulgation of "fake news" stories meant to hurt Democratic candidate Hillary ClintonHillary Rodham ClintonCongress wants Trump Jr. phone records related to Russian Federation meeting Zuckerberg hires top Clinton pollster amid rumors of presidential run: report Democrats" new "Better Deal' comes up short for people of color MORE and undermine faith in the US democracy.
Yet in April, Trump ordered military action against Russian-backed Syrian forces to punish the use of chemical weapons.
Until the sanctions bill, that is.