The Sea Shepherd Conservation Society engages in various demonstrations, campaigns, and tactical operations at sea and elsewhere, including conventional protests and direct actions to protect marine wildlife. Sea Shepherd operations have included interdiction against commercial fishing, shark poaching and finning, seal hunting and whaling. Many of their activities have been called piracy or terrorism by their targets and by the ICRW. Sea Shepherd says that they have taken more than 4,000 volunteers on operations over a period of 30 years.

Fishing (1987–present) Anti-driftnet campaigns (1987–present) Sea Shepherd engaged in a multi-year campaign against driftnetting practices, which it calls a way of strip mining the ocean's wildlife.

Sea Shepherd's Divine Wind vessel investigated suspected driftnet fleets and collected ghost nets in 1987 along the coast of southern Alaska.

In 1990, Sea Shepherd consulted with a physicist and found a successful way of sinking driftnets without causing ecological damage.

In 1990, Sea Shepherd travelled to the North Pacific with the intent of bringing driftnetting to public attention. While there, they found two Taiwanese driftnetters, which they filmed catching seabirds and dolphins in their nets. They rammed the power blocks, used to retrieve the nets. The ships were forced to head home, and no charges were brought against Sea Shepherd for the incident.

In 1991, Sea Shepherd learned that driftnetters were destroying the seabird and fish populations off of the coasts of Trinidad and Tobago. They travelled there and patrolled the area near the mouth of the Amazon. They encountered a driftnetting ship and threw stink bombs on its deck. The ship rammed the Sea Shepherd II, and they rammed the driftnetter back, leading to a confrontation that severely damaged both ships. Back in Trinidad, Sea Shepherd revealed that corrupt officials were taking bribes to turn a blind eye to driftnetting in the area, and the corrupt officials were removed from office. Sea Shepherd later donated four assault rifles to help the Coast Guard chase driftnetters.

In 1992, Sea Shepherd returned to fight driftnetters in the North Pacific. They encountered a fleet of Japanese driftnetters. They chased one away, and fired air cannons and fire crackers at another to slow it down. However, no ramming took place because the fishermen on deck would not move. They did manage to retrieve a cargo hold of driftnet and create an international incident.

In 1992, Sea Shepherd agent Dwight Worker covertly entered Taiwan. While there, he sank the driftnetting ship Jiang Hai in harbor. He also documented thousands of miles of driftnet being added to 43 driftnetting vessels, despite a ban on ships being outfitted with new net.

Shepherd only reduced their campaign activities after the United Nations in 1992 banned driftnetting, but they did not stop their campaigns.

In 1995, Sea Shepherd convinced the government of Ireland to disallow driftnetting in their territorial waters.

In 1997, Sea Shepherd announced a campaign to fight driftnetting in the Mediterranean. Italy's driftnetters, the primary suspects, immediately halted the practice.

Sea Shepherd in 2006 noted that drift netting had again gained prominence, due to the reduction of fish stocks tempting commercial fisheries to again use the method to keep up their catch volumes.

In March 2016, Sea Shepherd announced the launch of Operation Driftnet, to combat illegal fishing in the Indian Ocean and subsequently employ direct-action techniques to shut-down their operations. They found and engaged a fleet of 6 driftnetters, and 3 of the ships were arrested for illegal fishing.

Tuna boat killing of dolphins (1988–1989, 1991–1992) In 1988, Sea Shepherd released footage of dolphins being killed by an American-owned tuna seiner. The film was edited by Peter Brown. The footage scandalized the tuna industry and led to a ban on dolphin killing by U.S. tuna companies.

In 1989, Sea Shepherd travelled to Costa Rica to ram a tuna seiner and bring the issue to public attention. They found a tuna seiner called the Pan Pacific, which they confirmed had been illegally killing dolphins. The ramming was eventually called off due to a dispute between Paul Watson and Scott Trimmingham. Scott said that ramming would upset his negotiations to have tuna fishing banned in Costa Rica, to which Watson replied that they created international incidents—they didn't negotiate. In the end, they boarded the Pan Pacific and inspected the logbook, which revealed locations where dolphins were being killed. Using the information, they travelled along the Mexican coast and stopped several tuna seiners from various Latin American countries from killing dolphins.

In February 1991, representatives of a tuna boat in the Pacific south of Mexico said that they had been rammed by Sea Shepherd II. Sea Shepherd accused it of catching and killing dolphins in its tuna nets and confirmed its ship had dealt the tuna boat a "glancing blow." They had originally planned to destroy the fishermen's small boat used to lay nets, but called the plan off because the fishermen were too close. They also turned a fire hose on the fishermen's helicopter (used to herd the dolphins) in order to ensure costly repairs.

In 1992, Sea Shepherd launched another campaign to stop tuna seiners from killing dolphins. They stopped in Mexico to repair their ship, Sea Shepherd II. Despite warnings from the Mexican navy that they would be arrested due to the incident the previous year, they entered the country and covertly did repairs with no incident. They later stopped a tuna seiner from killing a pod of dolphins off of Mexico.

Cooperation with Costa Rica (2002) In April 2002, the government of Costa Rica invited Sea Shepherd to assist in patrolling for poachers around Cocos Island. The group and Costa Rica had negotiated an agreement for this work which was due to be finalised on April 30, 2002. On April 22, the Farley Mowat (formerly the Ocean Warrior), captained by Paul Watson, was en route to the island when it came across the Varadero I which the group alleges was poaching sharks. The authorities were contacted and Sea Shepherd was told to bring the ship in. The Farley Mowat forced the other vessel into a nearby Guatemalan port with the use of pressure hoses, and in the altercation, the two vessels collided, causing some damage to the Varadero I.

Subsequently, Watson was charged with attempted shipwrecking and murder by the fishermen. These charges were dropped on April 29 by the prosecutor when footage of the incident taken by a documentary team aboard the Farley Mowat was shown. Footage of the event can be seen in the film Sharkwater. The prosecutor was reported to have found no evidence of any wrongdoing. A new prosecutor was later appointed to repursue the charges and Watson's lawyer advised he leave the country. Local environmental groups argue that fishing interests opposed to marine conservation were behind the legal proceedings. After subsequent litigation against the judges and prosecutors in Costa Rica, the criminal charges were dismissed in 2019.

Sea Shepherd had previously worked to protect Cocos Island. In 1992, they chased over a dozen poachers out of the marine reserve with flares, water cannons, pie cannons, stink bombs, paintball guns, and air from a Civil War-Era cannon. Footage of the poachers was sent to the Costa Rican authorities, and several of the poachers were later arrested. In 2001, Sea Shepherd captured the poacher San José 1. The vessel was arrested and later confiscated.

Southern Pacific/Galápagos Islands (2000–present) The Sea Shepherd Conservation Society has operated in the Galápagos marine reserve to protect marine wildlife. The reserve was declared in 1986, with an increased area declared in 1998, and despite government attempts to limit catches, fishing continued in the waters around the Galápagos Islands. The Galápagos National Park Directorate lacked the manpower to adequately manage the marine park, and fishing laws were regularly flouted. The largest fisheries were for spiny lobster, sea cucumbers, and shark fins, mainly for export to Asian markets. Longline fishing and illegal nets also cause a bycatch of seals, turtles, sharks, boobies and other marine animals.

In December 2000, the Sea Shepherd ship, Sirenian, was sent to the Galápagos to assist in patrolling the 130,000 square kilometre marine reserve around the Islands. Sea Shepherd had signed a five-year agreement with the Galápagos National Park Directorate to provide the Sirenian, with some crew, as a patrol vessel. Under the agreement, the Sirenian had an Ecuadorian captain, engineer, and carries Park Service officers. The Sirenian is a 95-foot former United States Coast Guard Cutter and is now permanently stationed in the Galápagos.

In November 2000, the fishers reacted to new catch limits on lobster by ransacking the Park Service offices, the facilities of the Darwin Research Centre and trashing the park director's home, burning his possessions in the street. The Sirenian carried a cargo of new computers, cameras, and communications equipment to replace what was destroyed by the fishers. The Sirenian captured four illegal boats in the first three weeks of March, 2001.

In September 2001, the Ecuadorian Navy detained the Ocean Warrior. This occurred after the Park Service captured seven illegal shark fishing boats at sea and Sea Shepherd criticized the Ecuadorian Navy for not enforcing the law. The Sea Shepherd Ecuadorian representative, Sean O'Hearn-Giminez, was arrested onboard and threatened with deportation.

In June 2004, a Sea Shepherd crew-member, Cathy Davies, along with at least six other Sea Shepherd members, was taken hostage during protests by fishers who were protesting recently enacted quotas on sea cucumber (Holothuroidea). Armed with clubs, pipes, and Molotov cocktails, the fishers had seized Park Service offices and tourist locations. Sea Shepherd crew joined Park Services officers at the barricades erected by fishers around the buildings. Another team of Sea Shepherd crew were dispatched to guard Lonesome George, one of the Galápagos Islands' most famous turtles, as the fishers had threatened to kill him if the quota on sea cucumber was not lifted. About 100 residents of San Cristóbal Island marched in protest against the fishers actions. In July, the High Court of Ecuador upheld the Park Service limits on the take of sea cucumber. The Park Service banned the catch of sea cucumber for 2005 and 2006 to allow for the populations to recover from over-fishing. Watson called this a "great victory for conservation in the Galápagos." In an agreement with the World Wildlife Fund, Sea Shepherd donated the Sirenian to the Galápagos National Park Service. The WWF refurbished the boat, which now operates as the Yoshka.

In May 2007, the president of Ecuador, Rafael Correa, relaxed an International ban on shark finning by legalizing the sale of fins from sharks caught accidentally. Sea Shepherd's Ecuadorian representative, Sean O'Hearn-Giminez, accompanied a police raid that found two tons of sharks fins caught before a Presidential decree. Fifteen people were arrested in the raid at Manta. However, a prosecutor ordered them released and the shark fins were returned to the fishers. O'Hearn-Giminez was arrested and ordered to be deported. This order was revoked later that day at the request of President Correa. The reason given was that O'Hearn-Giminez had a valid visa, as his wife is Ecuadorian.