The President paused in his remarks and then responded, "To my fellow citizens, we believe in free speech in the United States of America."
One woman moved towards the stage before being stopped by security, but other protesters still made their voices heard.
Only minutes later, another protester shouted expletives at the President, while still another called Bush "a fascist".
By the time Bush finished his 10-minute remarks, at least nine protesters had been escorted out of the event by law enforcement.
Although Bush did not mention the wars in Iraq and Afghanistan in his final Fourth of July speech as President, he did thank the troops, while paying tribute to the author of the Declaration of Independence, who died on this day in 1826.
"We honor Jefferson's legacy by aiding the rise of liberty in lands that do not know the blessings of freedom," Bush said. "And on this Fourth of July we pay tribute to the brave men and women who wear the uniform of the United States of America," prompting a standing ovation from the assembled crowd.
Bush congratulated the new citizens participating in the naturalization ceremony, more than 70 men and women from about 35 different countries, including Iraq, Afghanistan, Norway, and Burma.
"From this day forward the history of the United States will be part of your heritage, the Fourth of July will be part of your Independence Day, and I will be honored to call you a fellow American," said the President.
While in Charlottesville, Bush toured Monticello with Virginia Governor Tim Kaine, a Democrat. Early in the afternoon, Bush returned to the White House to celebrate Independence Day, a holiday which falls right at the start of his birthday weekend.
"Thomas Jefferson once said he'd rather celebrate the Fourth of July than his own birthday," said Bush, who turns 62 on Sunday. "To me it's pretty simple, the Fourth of July weekend is my birthday weekend."
Protesters also lined the President's motorcade route, chanting "Arrest Bush" as he drove to and from the Monticello ceremony.
Copyright © 2008 ABCNews Internet Ventures