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 Northwest.
In 1987, Kennedy founded the Environmental Litigation Clinic at Pace University School of Law, where for three decades he was the clinic's supervising attorney and co-director, and as Clinical Professor of Law. Kennedy obtained a special order from the New York State Court of Appeals that permitted his 10 clinic students–second- and third-year law students–to practice law and to try cases against Hudson River polluters in state and federal court, under the supervision of Kennedy and his co-director, Professor Karl Coplan. The clinic's full-time clients are Riverkeeper and Long Island Soundkeeper.
In June 1999, as Riverkeeper's success on the Hudson began inspiring the creation of Waterkeepers across North America, Kennedy and a few dozen Riverkeepers gathered in Southampton, Long Island, to found the Waterkeeper Alliance, which is now the umbrella group for the 344 licensed Waterkeeper programs located in 44 countries. As President of the Alliance, Kennedy oversees its legal, membership, policy and fundraising programs. The Alliance states that it is dedicated to promoting "swimmable, fishable, drinkable waterways, worldwide," and is also a clearinghouse, approving new Keeper programs and licensing use of the trademarked "Waterkeeper," "Riverkeeper," "Soundkeeper," "Lakekeeper," "Baykeeper," "Bayoukeeper," "Canalkeeper," "Coastkeeper," etc. names.
In 2000, Kennedy and environmental lawyer Kevin Madonna founded the environmental law firm Kennedy & Madonna, LLP, to represent private plaintiffs against polluters. The firm litigates environmental contamination cases on behalf of individuals, non-profit organizations, school districts, public water suppliers, Indian tribes, municipalities and states. In 2001, Kennedy & Madonna organized a team of prestigious plaintiff law firms to challenge pollution from industrial pork and poultry production. In 2004, the firm was part of a legal team that secured a $70 million settlement for property owners in Pensacola, Florida whose properties were contaminated by chemicals from an adjacent Superfund site.
In 2013, Kennedy and his partner sold the brand to Nestlé in exchange for a donation to local Waterkeepers.
Kennedy was a co-owner and Director of the smart grid company Utility Integration Solutions (UISol), which was acquired by Alstom. He is presently a co-owner and Director of GridBright, the market-leading grid management specialist. In October 2011, Kennedy co-founded EcoWatch, an environmental news site.
In his first case as an environmental attorney, Kennedy represented the NAACP in a lawsuit against a proposal to build a garbage transfer station in a minority neighborhood in Ossining, New York.