In Washington, President Barack Obama planned to observe the anniversary with a private moment of silence at the White House.
"Today, we recognize the incredible courage and leadership of so many Bostonians in the wake of unspeakable tragedy," Obama said in a statement. "And we offer our deepest gratitude to the courageous firefighters, police officers, medical professionals, runners and spectators who, in an instant, displayed the spirit Boston was built on — perseverance, freedom and love."
Obama said this year's race, scheduled for Monday, will "show the world the meaning of Boston Strong as a city chooses to run again."
Earlier in the day, a wreath-laying ceremony drew the families of the three people killed — Martin Richard, Krystle Campbell and Lu Lingzi — as well as relatives of Massachusetts Institute of Technology police Officer Sean Collier, who was killed in the aftermath of the blasts.
Gov. Deval Patrick, Mayor Martin J. Walsh and Boston Cardinal Sean O'Malley were among those who attended the morning ceremony held in a light rain as bagpipes played. O'Malley offered a prayer.
At the Hynes center, Vice President Joe Biden was on hand to honor the victims later. Several survivors also spoke, including newlywed Patrick Downes and dancer Adrianne Haslet-Davis, both of whom lost their lower left legs in the bombings.
"We should have never met this way, but we are so grateful for each other," Downes said, describing the sense of community that has developed among those who lost limbs and were otherwise injured.
Carlos Arredondo, the cowboy hat-wearing spectator who was hailed as a hero for helping the wounded after the bombings, said he came to the tribute ceremony to support survivors and their families.
"You can see how the whole community gathered together to support them and remember," he told reporters before the program began.
Boston police Commissioner Williams Evans said the anniversary is an emotional day and brings back "some terrible memories."
"Hopefully, today brings the city and the families some sense of comfort and some healing," he said before ceremonies began.
Between 2:30 p.m. and 3 p.m., a flag-raising ceremony and moment of silence will be held at the marathon finish line, to mark the time and place where two bombs exploded on April 15, 2013.
Authorities say two brothers planned and orchestrated the attack and later shot and killed Collier during an attempt to steal his gun. Tamerlan Tsarnaev, 26, died following a shootout with police several days after the bombings. Dzhokhar Tsarnaev, 20, has pleaded not guilty to 30 federal charges and is awaiting trial. He faces the possibility of the death penalty.
The Tsarnaevs, ethnic Chechens who lived in the former Soviet republic of Kyrgyzstan and the Dagestan region of Russia, settled in Cambridge, outside Boston, more than a decade ago after moving to the U.S. as children with their family.
Prosecutors have said Dzhokhar Tsarnaev left a hand-scrawled confession condemning U.S. actions in Muslim countries on the inside wall of a boat he was found hiding in following the police shootout.