Hundreds filed past the open coffin of Ethel Lance, 70, at a funeral home in North Charleston yesterday, ahead of an afternoon service for Sharonda Singleton, 45.
The deceased were among the Bible study group that was targeted in the June 17 massacre at the historic Emanuel African Methodist Episcopal Church.
Dylann Roof, 21, is charged with murder in connection with the multiple killings, which he reportedly hoped would trigger a race war between blacks and whites.
Obama will also meet the families of some of the other victims.
There was raw emotion at the Royal Missionary Baptist Church as friends and relatives bid a final farewell to Lance, a custodian at a Charleston arts center.
"I am here to tell you that we are stronger because we are together as a community," Reverend Norvell Goff told the mourners, the local Post and Courier newspaper reported.
Lance was later laid to rest at the Emanuel cemetery, where her children and grandchildren kissed her coffin and well-wishers threw roses into her grave.
"She believed she could change every child," said South Carolina Governor Nikki Haley, who attended both funeral services.
Seen in the pews were Jesse Jackson and Al Sharpton, two of the most recognizable civil rights activists in the United States today.
Obama "will be mindful of not just how sad it is that those individuals were taken from us, but also use the occasion to celebrate their lives," White House spokesman Josh Earnest said.
"Many of them, in the way that they went about their day-to-day lives, I do think serve as a genuine inspiration to others about the way that they lived their lives and about the values that they sought to embody.
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