The marine park exists because of a geological accident. The Saguenay Fjord, one of the longest and southernmost fjords in the Northern Hemisphere, channels cold, dense water from inland Quebec into the St. Lawrence estuary. Where these two bodies of water collide, the difference in temperature and salinity forces deep, nutrient-laden water up toward the surface. This upwelling creates an underwater meadow of phytoplankton and krill that ripples through the entire food chain. Microscopic algae feed tiny crustaceans. Crustaceans feed fish. Fish feed seals. And the krill itself, in concentrations so thick they cloud the water, feeds the largest animals that have ever lived. The park encompasses three distinct marine ecosystems: the middle estuary of the St. Lawrence, the lower estuary, and the Saguenay Fjord itself. Species migrate freely between all three zones, following the food as currents shift with the tides and seasons. More than 2,000 wild species inhabit these waters, from microscopic organisms to the blue whale.

The St. Lawrence beluga population is the park's most iconic and most imperiled resident. These small, vocal whales, nicknamed the canaries of the sea for their constant calls and clicks, are one of only two marine mammal species that live in the park year-round, along with the harbour seal. The beluga population here is geographically and reproductively isolated from all other beluga populations in the world, making it effectively endemic to the St. Lawrence. Numbering approximately 900 individuals, this population was designated as endangered by COSEWIC. The park's territory generally covers the critical habitat of the St. Lawrence beluga, and protecting these animals was among the most compelling reasons for the park's creation. In summer, belugas gather in the warmer, shallower waters near the Saguenay's mouth to nurse their calves, the grey juveniles swimming close beside their white mothers in tight family groups. The sight of dozens of belugas surfacing in unison, their exhalations creating small clouds above the dark water, has made this stretch of river one of the most celebrated whale-watching destinations on the planet.

The marine park did not happen by accident. In 1988, Father Rosaire Corbin assembled a Coalition for the creation of the Saguenay-Saint-Laurent marine park, uniting 27 regional organizations behind a single goal. That same year, the International Forum for the Future of the Beluga brought together scientists, conservationists, and government officials who argued that without protected habitat, the endangered beluga population would continue to decline. The political momentum built through the early 1990s, and in 1997 the Government of Quebec passed the law establishing the marine park. It became operational in 1998. The park is managed jointly by SEPAQ and Parks Canada, a rare federal-provincial partnership that reflects the jurisdictional complexity of protecting marine ecosystems that cross political boundaries. Humans have frequented these shores for roughly 8,000 years, as archaeological artefacts attest. First Nations peoples hunted seals at Cap Bon-Desir and traded along the St. Lawrence long before Europeans arrived. The inhabitants of New France continued the marine hunting traditions they found already in place.

Nine species of marine mammals regularly frequent the park. Beyond the year-round belugas and harbour seals, summer brings an extraordinary procession of migratory visitors: grey seals, harp seals, harbour porpoises, minke whales, fin whales, humpback whales, and the blue whale, the largest animal ever to have existed. Whale-watching excursions depart from Tadoussac, Baie-Sainte-Catherine, and the Port of Quebec, with zodiac boats and larger cruise vessels navigating under strict regulations designed to minimize disturbance to the animals. From shore, the observation points at Les Escoumins and along the coast between La Malbaie and Tadoussac offer vantage points where the marine relief drops to sufficient depth that whales feed close enough to see without binoculars. The park is adjacent to Fjord-du-Saguenay National Park on its landward side, and together the two protected areas form a continuous conservation corridor from the heights of the fjord cliffs down to the cold, dark seabed where the food chain begins.