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.
His nomination as vice president on Kennedy's ticket drew her deep into a national campaign. She stumped through 11 Southern states, mostly alone, making speeches at whistle stops in her soft drawl. In his 1965 memoir, "Kennedy," JFK special counsel Theodore Sorensen recalled her "remarkable campaign talents" in the 1960 campaign.
She was with her husband in Dallas on Nov. 22, 1963, when Kennedy was assassinated, and was at his side as he took the presidential oath of office aboard Air Force One.
In her book "A White House Diary," she recalled seeing Jacqueline Kennedy with her husband's blood still on her dress and leg. "Somehow that was one of the most poignant sights — that immaculate woman, exquisitely dressed, and caked in blood," she wrote.
Suddenly, the unpretentious woman from Texas found herself first lady of the United States, splitting time between the White House and the Johnson family's 13-room stone and frame house on the LBJ Ranch, near Johnson City west of Austin.
Her White House years also were filled with the turbulence of the Vietnam War era.
The first lady often would speak her fears and hopes into a tape recorder, and some of the transcripts were included in the 2001 book "Reaching for Glory, Lyndon Johnson's Secret White House Tapes, 1964-1965," edited by historian Michael Beschloss.
"How much can they tear us down?" she wondered in 1965 as criticism of the Vietnam War worsened. "And what effect might it have on the way we appear in history?"
She quoted her husband as saying: "I can't get out. And I can't finish it with what I have got. And I don't know what the hell to do."
Lady Bird Johnson served as honorary chairwoman of the national Head Start program and held a series of luncheons spotlighting women of assorted careers and professions.
Both daughters married while their father was president. Luci married Patrick Nugent, in 1966 at the Shrine of the Immaculate Conception in Washington. That marriage ended in divorce and she wed Canadian banker Ian Turpin in 1984. Daughter Lynda Bird married Charles Robb, later governor and U.S. senator from Virginia, in a White House wedding in 1967.
After she and her husband left Washington, Lady Bird Johnson worked on "A White House Diary," published in 1970. She also served a six-year term starting in 1971 as a University of Texas regent.
She and her daughters remained active in her wildflower advocacy and with the LBJ Library in Austin after the former president's death in 1973. Into her 90s, Lady Bird Johnson made occasional public appearances at the library and at civic and political events, always getting a rousing reception.
President Gerald Ford appointed her to the advisory council to the American Revolution Bicentennial Administration, and President Jimmy Carter named her to the President's Commission on White House Fellowships. Her long list of honors and medals include the country's highest civilian award, the Medal of Freedom, bestowed in 1977 by Ford.
She was born Claudia Alta Taylor on Dec. 22, 1912, in the small East Texas town of Karnack. Her father was Thomas Jefferson Taylor, a wealthy rancher and merchant. Her mother was the former Minnie Lee Patillo of Alabama, who loved books and music.
Lady Bird Johnson received her nickname in infancy from a caretaker nurse who said she was as "pretty as a lady bird." It was the name by which the world would come to know her. She disliked it, but said later, "I made my peace with it."
When Lady Bird was 5, her mother died, and her aunt, Effie Patillo, came to care for her and two older brothers.
She graduated from Marshall High School at age 15 and prepared for college at St. Mary's Episcopal School for Girls in Dallas. At the University of Texas in Austin she studied journalism and took enough education courses to qualify as a public school teacher. She received a bachelor of arts degree in 1933 and a bachelor of journalism in 1934.
A few weeks later, through a friend in Austin, she met Lyndon Johnson, then secretary to U.S. Rep. Richard Kleberg, a Democrat from Texas. The day after their first date, Lyndon Johnson proposed. They were married within two months, on Nov. 17, 1934, in San Antonio.
Lyndon Johnson caught the eye of Congressman Sam Rayburn of Texas, who later became the U.S. House speaker. Rayburn persuaded President Franklin D. Roosevelt in 1935 to appoint Johnson director of the National Youth Administration for Texas.
When Rep. James Buchanan, D-Texas, died two years later, Johnson ran for the House seat. His wife borrowed $10,000 from her father to finance the campaign, and Johnson won easily.
Johnson lost a 1941 special election for the U.S. Senate, but narrowly won the seat in 1948, after he was declared the victor by just 87 votes in a Democratic primary runoff against former Gov. Coke Stevenson.
In December 1972, the Johnsons gave the LBJ Ranch house and surrounding property to the United States as a National Historic Site, retaining a life estate for themselves. The property is to transfer to the federal park service after her death.
The family's privately held broadcasting company — later overseen by Luci Baines Johnson — was sold in March 2003 to Emmis Communications of Indianapolis. Lady Bird Johnson had been a director of the radio company in her later years and even attended most board meetings before her 2002 stroke.
On her 70th birthday, in 1982, she and Helen Hayes founded the National Wildflower Research Center near Austin, later renamed the Lady Bird Johnson Wildflower Center. The research and education center is dedicated to the preservation and use of wildflowers and native plants.
"I'm optimistic that the world of native plants will not only survive, but will thrive for environmental and economic reasons, and for reasons of the heart. Beauty in nature nourishes us and brings joy to the human spirit," Lady Bird Johnson wrote.
In addition to her two daughters, survivors include seven grandchildren, a step-grandchild, and several great-grandchildren.