Protests and clashes have flared for years in the tiny but strategic island nation between the Sunni-led monarchy and Bahrain's majority Shiite population, which has complained of discrimination and other abuses. Bahrain hosts the U.S. Navy's 5th Fleet.
The timing of the raid was striking, coming two days after President Trump publicly assured the king of Bahrain that their relationship would be free of the kind of "strain" that had occurred in the past — an apparent reference to the Obama administration's periodic chiding of Bahrain over its human rights violations.
"Our countries have a wonderful relationship together, but there has been a little strain, but there won't be strain with this administration," Trump said during a photo session with the king, Hamad bin Isa al-Khalifa, at a conference in Riyadh, Saudi Arabia.
Trump's attendance at the Riyadh conference was largely aimed at winning back Persian Gulf allies that had bristled at President Barack Obama's outreach to Shiite power Iran.
Trump's widely anticipated speech, ostensibly about Islam and extremism, included assurances to the gulf's Sunni states that "our friends will never question our support."
In Washington, the State Department said that it is "troubled" by the clashes and urged restraint on all sides. "We urge the government of Bahrain to ensure those arrested are provided with access to counsel and that legal proceedings are conducted with transparency in accordance with due process," spokeswoman Heather Nauert said in a statement.
Bahrain's Ministry of Information Affairs did not immediately respond to a request for more details on the circumstances that led to the deaths or about the evolving U.S. relationship with Bahrain. A government statement released Wednesday said protesters refused an order to disperse and injured security personnel. It said the deaths were being investigated by the public prosecutor.
Members of Bahrain's Shiite majority have long protested what they say is widespread discrimination at the hands of the Sunni dynasty ruling the country.