Johnson, who suffered a stroke in 2002 that affected her ability to speak, returned home late last month after a week at Seton Medical Center, where she'd been admitted for a low-grade fever.
She died at her Austin home of natural causes and she was surrounded by family and friends, said spokeswoman Elizabeth Christian.
Even after the stroke, Johnson still managed to make occasional public appearances and get outdoors to enjoy her beloved wildflowers. But she was unable to speak more than a few short phrases, and more recently did not speak at all, Anne Wheeler, spokeswoman for the LBJ Library and Museum, said in 2006. She communicated her thoughts and needs by writing, Wheeler said.
The longest-living first lady in history was Bess Truman, who was 97 when she died in 1982.
Johnson was born Claudia Alta Taylor in 1912. A nurse called her "Lady Bird," a nickname she hated, but it stuck, reports CBS News' Harry Smith.
The daughter of a Texas businessman, Johnson grew up to be one of the country's most influential environmentalists. After her mother died when she was 5, she found comfort in the beauty of the Texas landscape, reports Smith.
"I knew all the trees and brooks and back country roads within walking distance of my home," she once said in an interview with CBS News.
She planned to be a newspaper reporter — until she met Lyndon Baines Johnson. He proposed after their first date. Ten weeks later, she said yes, reports Smith. Johnson used part of her inheritance to back her husband's first political campaign for a seat in the House.
She spent 34 years in Washington, as the wife of a congressional secretary, U.S. representative, senator, vice president and president. The couple had two daughters, Lynda Bird, born in 1944, and Luci Baines, born in 1947. The couple returned to Texas after the presidency, and Lady Bird Johnson lived for more than 30 years in and near Austin.
"She truly was the most influential advisor around Lyndon Johnson," said CBS News chief Washington correspondent Bob Schieffer. "She was a part of the Lyndon Johnson presidency as no other person was."
"Lady Bird Johnson was a wonderful first lady and one of the kindest and most caring and compassionate people I've ever met in politics," said Senator Edward M. Kennedy in a statement released today. "She was a great friend to the Kennedy family, in both good times and bad, and we cherished every moment we spent with her. May God bless her and her entire family."
Other former first ladies remembered Johnson on Wednesday as deeply devoted to her family and the environment.
"Her beautification programs benefited the entire nation. She translated her love for the land and the environment into a lifetime of achievement," Betty Ford said.
Nancy Reagan said that when Lyndon Johnson was called upon to take the oath of office in the face of tragedy after the assassination of John F. Kennedy, "he did so with his courageous wife beside him." She said Lady Bird Johnson served the nation with honor and dignity.
"I believe above all else that Lady Bird will always be remembered as a loyal and devoted wife, a loving and caring mother and a proud and nurturing grandmother," Reagan said.
"I think we all love seeing those we love loved well, and Austin has loved my mother very well. This community has been so caring," Luci Baines Johnson said in an interview with The Associated Press in December 2001.
"People often ask me about walking in her shadow, following in the footsteps of somebody like Lady Bird Johnson," she said. "My mother made her own unique imprint on this land."
Former President George H.W. Bush once recalled that when he was a freshman Republican congressman from Texas in the 1960s, Lady Bird Johnson and the president welcomed him to Washington with kindness, despite their political differences.
He said she exemplified "the grace and the elegance and the decency and sincerity that you would hope for in the White House."
"Like all Americans, but especially those of us who call Texas home, we loved Lady Bird," Bush said Wednesday.
As first lady, she was perhaps best known as the determined environmentalist who wanted roadside billboards and junkyards replaced with trees and wildflowers. She raised hundreds of thousands of dollars to beautify Washington. The $320 million Highway Beautification Bill, passed in 1965, was known as "The Lady Bird Bill," and she made speeches and lobbied Congress to win its passage.
"Had it not been for her, I think that the whole subject of the environment might not have been introduced to the public stage in just the way it was and just the time it was. So she figures mightily, I think, in the history of the country if for no other reason than that alone," Harry Middleton, retired director of the LBJ Library and Museum, once said.
Lady Bird Johnson once turned down a class valedictorian's medal because of her fear of public speaking, but she joined in every one of her husband's campaigns. She was soft-spoken but rarely lost her composure, despite heckling and grueling campaign schedules. She once appeared for 47 speeches in four days.
"How Lady Bird can do all the things she does without ever stubbing her toe, I'll just never know, because I sure stub mine sometimes," her husband once said.
Lady Bird Johnson said her husband "bullied, shoved, pushed and loved me into being more outgoing, more of an achiever. I gave him comfort, tenderness and some judgment — at least I think I did."
She had a cool head for business, turning a modest sum of money into a multimillion-dollar radio corporation in Austin that flourished under family ownership for more than a half-century. With a $17,500 inheritance from her mother, she purchased a small, faltering radio station in 1942 in Austin. The family business later expanded into television and banking.
"She was very hands on. She literally mopped the floor, and she sold radio time," daughter Luci Baines Johnson said of her mother's early days in business.
When Johnson challenged Sen. John F. Kennedy unsuccessfully in 1960 for the Democratic presidential nomination, his wife was his chief supporter, although she confessed privately she would rather be home in Texas.