Kennedy was born in Washington, D.C on January 17, 1954. He is the third of eleven children of Senator and Attorney General Robert Francis "Bobby" Kennedy and Ethel Skakel Kennedy, and is a nephew of Joseph Patrick "Joe" Kennedy Jr., U.S. President John Fitzgerald "Jack" Kennedy, and longtime Senator Edward Moore "Ted" Kennedy. His aunt Eunice Kennedy Shriver founded Special Olympics, and another aunt, Jean Kennedy Smith, is a former US ambassador to Ireland.

Kennedy was 9 years old when his uncle, President John F. Kennedy, was assassinated during a political trip to Dallas, and 14 years old when his father was assassinated while running for President in the 1968 Democatic presidential primaries. Kennedy learned of his father's shooting when he was at his Jesuit boarding school in North Bethesda, Maryland. A few hours later he flew out to Los Angeles on vice-president Hubert Humphrey's plane along with his elder sister Kathleen and elder brother Joseph, and was with his father when he died. Kennedy served as a pallbearer in his father's funeral, where he spoke and read excerpts from his father's speeches at the Mass commemorating his death at Arlington National Cemetery. Following his father's death, he was arrested for loitering and marijuana possession.

Kennedy has written extensively on foreign policy issues, beginning with a 1974 Atlantic Monthly article entitled, "Poor Chile," discussing the overthrow of Chilean President, Salvador Allende. Kennedy also wrote editorials against the execution of Pakistan President Zulfikar Ali Bhutto by General Muhammad Zia-ul-Haq. In 1975, he published an article in The Wall Street Journal, criticizing the use of assassination as a foreign policy tool. In 2005, he wrote an article for the Los Angeles Times decrying President Bush's use of torture as anti-American. Senator Edward Kennedy entered the article into the Congressional Record.

Kennedy is also a whitewater Kayaker. His father introduced him and his siblings to whitewater kayaking during early trips down the Green and Yampa Rivers in Utah and Colorado, the Columbia River, the Middle Fork Salmon in Idaho, and the Upper Hudson Gorge. From 1976 to 1981, Kennedy was a partner and guide at a white water company, "Utopian," based in West Forks, Maine. He organized and led several "first-descent" white-water expeditions to Latin America including three to hitherto unexplored rivers: the Apurimac, Peru, in 1975; the Atrato, Colombia, in 1979; and the Caroni,Venezuela, in 1982. He made an early descent of Great Whale River in Northern Quebec, in 1993, and has made many trips to Patagonia, Chile to run the Biobío River, the Futaleufú and other whitewater rivers.

Kennedy served on the National Staff and as a State Coordinator for Edward M. Kennedy for President from 1979 to 1980. Prior to that he had served on Senator Kennedy's 1970 and 1976 Massachusetts Senatorial Campaigns. He was a co-founder and a former board member of the New York League of Conservation Voters.

Kennedy has been an opponent of conventional nuclear power, arguing that it is unsafe and not economically competitive. On June 15, 1981, he made international news when he spoke at an anti-nuclear rally at the Hollywood Bowl, with Stephen Stills, Bonnie Raitt and Jackson Browne.

Kennedy married Emily Ruth Black (b. 1957) on April 3, 1982. They had two children: Robert Francis "Bobby" Kennedy III (b. 1984) and Kathleen Alexandra "Kick" Kennedy (b. 1988). The couple separated in 1992 and divorced in 1994.

In 1983, at age 29, Kennedy was arrested in a Rapid City, South Dakota airport for heroin possession after a search of his carry-on bag uncovered 0.0064 oz of the drug. Kennedy entered a guilty plea to Presiding Judge Marshall P. Young, who sentenced him to two years' probation and 1,500 hours of community Service. Following his arrest, Kennedy voluntarily entered a drug treatment center.

Beginning in 1985, Kennedy helped develop NRDC's international program for environmental, Energy, and human rights. He worked on environmental issues across the Americas, and traveled regularly to Canada and Latin American to assist Indigenous tribes to protect their traditional homelands and to oppose large-scale Energy and extractive projects in remote wilderness areas.

Kennedy litigated and supervised environmental enforcement lawsuits on the east coast estuaries on behalf of Hudson Riverkeeper and the Long Island Soundkeeper, where he also served as a board member. Long Island Soundkeeper brought numerous lawsuits against cities and industries along the Connecticut and New York coastlines. In 1986, Kennedy won a landmark case against Remington Arms Trap and Skeet Gun Club in Stratford, Connecticut, that ended the practice of shooting lead shot into Long Island Sound. Kennedy also filed federal lawsuits to close the Pelham Bay landfill and the New York Athletic clubs, arguing that those facilities were interfering with public use of Long Island Sound. On the Hudson, Kennedy brought a series of lawsuits against municipalities, including New York City, to properly treat sewage, and against industries, including, Consolidated Edison, General Electric and Exxon, to stop discharging pollution and to clean up legacy contamination.

In 1987, he successfully sued Westchester County, New York, to reopen the Croton Point park, which was heavily used primarily by poor and minority communities from the Bronx. He then forced the reopening of the Pelham Bay Park in the Bronx, which New York City had closed to the public and converted to a police firing range. Kennedy also led a battle to stop a plan to sell Washington D.C.'s Kingman Island—one of the rare National Parks in a minority neighborhood—to a private developer. In 2004, Kennedy and Riverkeeper successfully sued Exxon to clean up a large oil spill on Newton Creek in Greenpoint, Brooklyn.

Kennedy is a licensed master falconer, and has trained hawks since he was 11. He breeds hawks and falcons and is also licensed as a raptor propagator and a wildlife rehabilitator. He holds permits for Federal Game Keeper, Bird Bander, and Scientific Collector. He was President of the New York State Falconry Association from 1988 to 1991. In 1987, while serving on Governor Mario Cuomo's New York State Falconry Advising Committee, Kennedy authored the examination to qualify apprentice falconers given by New York State. Later that year he wrote the New York State Apprentice Falconer's Manual, which was published by the New York State Department of Environmental Conservation, and continues in use today.

Kennedy was a founding board member of the Food Allergy Initiative. His son Conor suffers from anaphylaxis Peanut allergies. Kennedy wrote the foreword to The Peanut Allergy Epidemic, in which he and the authors link increasing food allergies in children to certain vaccines that were approved beginning in 1989.

His campaigns helped block dams on Chile's Bio Bio and Futaleufu rivers in 1990 and 2016 respectively. In 2003, he mounted an ultimately unsuccessful battle against the building of a dam on the Macal River in Belize. Kennedy termed the Chalillo Dam "a boondoggle," and brought a high-profile legal challenge against a Canadian power company, Fortis Inc., the monopoly owner of Belize's electric utility. That case ultimately lost in a split decision by the Privy Council in London, UK, the supreme court of British Commonwealth Nations.

In 1991, Kennedy helped lead a campaign to block Hydro-Quebec from building the James Bay Hydro-project, a massive dam project in northern Quebec. He was credited with mobilizing US political Leaders and persuading New England lawmakers and New York officials, including New York Governor Mario Cuomo, to walk away from New York's multibillion-dollar contract with Hydro-Quebec. These actions helped to kill the project.

Kennedy has been a critic of environmental damage by the US military. In 1993, he successfully represented the Suquamish and Duwamish Indian tribes in a lawsuit against the U.S. Puget Sound Naval Shipyard in Bremerton, Washington, to stop polluting Puget Sound.

On April 15, 1994, Kennedy married Mary Kathleen Richardson (1959–2012) aboard a research vessel on the Hudson River. They had four children: John Conor Richardson Kennedy (b. 1994), Kyra LeMoyne Kennedy (b. 1995), william Finbar "Finn" Kennedy (b. 1997), and Aidan Caohman Vieques Kennedy (b. 2001). On May 12, 2010, Kennedy filed for divorce from Mary; three days later she was charged with drunken driving. On May 16, 2012, Mary was found dead in a building on the grounds of her Mount Kisco, New York, home. The Westchester County Medical Examiner ruled the death to be a suicide due to asphyxiation from hanging.

In 1995, Premier Ralph Klein of Alberta declared Kennedy persona non grata in the province due to Kennedy's activism against Alberta's large-scale hog production facilities. In 2002, Smithfield Foods filed a lawsuit against Kennedy in Poland, under a Polish law that makes criticizing a corporation illegal, after Kennedy denounced the company in a debate with Smithfield's Polish Director before the Polish parliament.

Between 1996 and 2000, Kennedy and NRDC helped Mexican commercial fishermen to halt Mitsubishi's proposal to build a salt facility in the Laguna San Ignacio, a gray whale breeding, calving and nursery area in Baja, Mexico. Kennedy wrote extensively against the project, and took the campaign to Japan, meeting with the Japanese Prime Minister, Keizo Obuchi.

In 1998, Kennedy, Chris Bartle and John Hoving created a bottled-water company, Keeper Springs, which donated all of its profits to Waterkeeper Alliance. In 2013, Kennedy and his partner sold the brand to Nestlé in exchange for a donation to local Waterkeepers.

In 1999, Kennedy hired william Wegner to work for Riverkeeper. He was a fishery scientist and falconer who had been sentenced to five years in prison; he served three years after pleading guilty to federal Criminal charges for smuggling bird eggs from Australia. In 2000, Robert Boyle, Riverkeeper's founder and former President, fired Wegner, citing his Criminal conviction, but Kennedy re-hired Wegner, believing he should be given a second chance. A majority of the Riverkeeper Board supported Kennedy's decision, but seven members joined Boyle in resigning.

Kennedy first considered running for political office in 2000, when New York Senator Moynihan announced he would not seek re-election to the U.S. Senate seat formerly held by Kennedy's father. His father was elected to the same seat in 1964, and held it for 41 months, until his death in 1968.

Under Kennedy's leadership, Waterkeeper launched its "Clean Coal is a Deadly Lie" campaign in 2001, bringing dozens of lawsuits targeting mining practices, which include mountaintop removal, slurry pond construction, and targeting mercury emissions and coal ash piles by coal burning utilities. Kennedy's Waterkeeper alliance has also been leading the fight against coal export, including from terminals in the Pacific North West.

In January 2003, Kennedy wrote a controversial article in The Atlantic Monthly entitled "A Miscarriage of Justice" about the 1975 murder of Martha Moxley in Greenwich, Connecticut. In the article, Kennedy insists that Michael Skakel's indictment "was triggered by an inflamed media, and that an innocent man is now in prison." Skakel and Kennedy are first cousins, as Kennedy's mother and Skakel's father are siblings. Kennedy's article presents the argument that there is more evidence suggesting that Kenneth Littleton, the Skakel family's live-in tutor, killed Moxley. He also calls Dominick Dunne the "driving force" behind Skakel's prosecution. In July 2016, Kennedy released a book entitled Framed: Why Michael Skakel Spent over a Decade in Prison for a Murder He Didn't Commit. In September 2017, the rights to Kennedy's book were optioned by FX Productions to develop a multi-part television series.

Throughout the presidency of George W. Bush, Kennedy was a persistent critic of Bush's environmental and Energy policies. He accused Bush of defunding and corrupting federal science projects. Kennedy's February 2004 article in The Nation, "The Jun K Science of George W. Bush," in which he wrote, "The Bush Administration's first instinct when it comes to science has been to suppress, discredit or alter facts it doesn't like," has been recognized by Project Censored among top censored stories in their 2005 compilation.

In 2005, Kennedy considered running for New York Attorney General. The possibility of a matchup against his then brother-in-law Andrew Cuomo generated media interest. Kennedy again decided not to run, despite being considered the frontrunner if he were to run.

Kennedy has been critical of the integrity of the voting process. In June 2006 he published an analysis in Rolling Stone magazine purporting to show that GOP operatives stole the 2004 election for President George W Bush. Kennedy's conclusions were strongly attacked by Farhad Manjoo in a June 3, 2006 Salon.com article. However, in a critical response to Monjoo's attack, Historian Eric Zuesse argued that Kennedy's analysis had been correct.

In late 2007, Kennedy and his sisters Kerry and Kathleen announced that they would be endorsing Hillary Clinton in the Democratic Presidential Primary. Following the Democratic Convention, Kennedy campaigned for Obama across the country. After the election, he was named as a front-runner for Obama's EPA administrator.

On December 2, 2008, Kennedy announced that he did not wish to be appointed to the U.S. Senate by New York Governor David Paterson. He felt that it would take too much time away from his family.

The clinic has prosecuted numerous governments and companies for polluting Long Island Sound and the Hudson River and its tributaries. The clinic argued cases to expand citizen access to the shoreline, and won hundreds of settlements for the Hudson Riverkeeper. Kennedy and his students also sued dozens of municipal waste-water treatment plants to force compliance with the Clean Water Act. In 2010, a Pace lawsuit forced ExxonMobil to clean up tens of millions of gallons of oil from legacy refinery spills in Newtown Creek in Brooklyn, New York.

In June 2005, Kennedy authored an article in Rolling Stone and Salon.com titled Deadly Immunity alleging a government conspiracy to conceal a connection between thimerosal and the epidemic of childhood neurodevelopmental disorders, including autism. The article contained five factual errors, leading Salon.com to issue corrections. Kennedy argued that the errors were insignificant and that some were made by Salon during the editing process. Six years later, on January 16, 2011, Salon retracted the article completely. According to Salon, the retraction was motivated by accumulating evidence of errors and scientific fraud underlying the vaccine-autism claim. Kennedy has accused Salon.com of caving into pressure from the pharmaceutical industries. Rolling Stone stands by Kennedy's story – as noted by Rolling Stone's editor: "The link to this much-debated story by Robert F. Kennedy Jr. was inadvertently broken during our redesign in the spring of 2010. (We did not remove the story from the site, as some have incorrectly alleged, nor ever contemplated doing so.)".

Kennedy has written frequent warnings about the ease of election hacking and the dangers of voter purges and voter ID laws. He wrote the introduction and a chapter in Billionaires and Ballot Bandits, a 2012 book on election hacking by investigative Journalist Greg Palast.

In September 2013, The New York Post released excerpts from Kennedy's stolen 2001 diary, in which Kennedy described multiple affairs, and penned his opinions about public figures. Kennedy said the paper had printed "...excerpts from a 13-year-old diary illegally stolen from me...".

Kennedy married his third wife, actress-director Cheryl Hines, on August 2, 2014, at the Kennedy compound in Hyannis Port, Massachusetts.

In 2015, he took two of his sons to the Yukon to visit Mount Kennedy and run the Alsek River, a whitewater river fed by the Alsek Glacier, which flows off Mt. Kennedy. Mt. Kennedy was the highest unclimbed peak in Canada, when the Canadian Government named it for the assassinated American President, in 1964. Kennedy's father, Robert Kennedy, was the first to climb Mt. Kennedy in 1965.

In an article entitled "Why the Arabs Don't Want Us in Syria," published in Politico in February 2016, Kennedy referred to the "bloody history that modern interventionists like George W. Bush, Ted Cruz and Marco Rubio miss when they recite their narcissistic trope that Mideast nationalists 'hate us for our freedoms.' For the most part they don't; instead they hate us for the way we betrayed those freedoms — our own ideals — within their borders." Kennedy blames the Syrian war on a pipeline dispute. He cites wiki-leaks documents alleging that the CIA led military and intelligence planners to foment a Sunni uprising against Syria's President, Bashar al-Assad, following his rejection of a proposed Qatar-Turkey pipeline through Syria in 2009, well before the Arab Spring. In 2013, Kennedy wrote an article for Rolling Stone exploring President John F. Kennedy's difficult struggle with his own military and intelligence apparatus to keep America out of war and from becoming an imperial state.

On February 15, 2017, Kennedy and actor Robert De Niro gave a press conference at the National Press Club in Washington D.C., in which they accused the press of acting as propagandists for the $35 billion vaccination industry and refusing to allow debates on vaccination science. They offered a $100,000 reward to any Journalist or other citizen who could point to a study showing that it is safe to inject mercury into babies and pregnant women at levels currently contained in flu vaccines.