The son of a pastor, Louis Agassiz was born in Môtier (now part of Haut-Vully) in the canton of Fribourg, Switzerland. Educated first at home, then spending four years of secondary school in Bienne where he entered in 1818, he completed his elementary studies in Lausanne. Having adopted Medicine as his profession, he studied successively at the universities of Zürich, Heidelberg and Munich; while there he extended his knowledge of natural history, especially of botany. In 1829 he received the degree of Doctor of philosophy at Erlangen, and in 1830 that of Doctor of Medicine at Munich. Moving to Paris he came under the tutelage of Alexander von Humboldt (and later his financial benevolence) Humboldt and Georges Cuvier launched him on his careers of geology and zoology respectively. Previously he had not paid special attention to the study of ichthyology, but it soon became the focus of his life's work.

In 1819–1820, Johann Baptist von Spix and Carl Friedrich Philipp von Martius were engaged in an expedition to Brazil, and on their return to Europe, amongst other collections of natural objects they brought home an important set of the fresh water fish of Brazil, and especially of the Amazon River. Spix, who died in 1826, did not live long enough to work out the history of these fish, and Agassiz, having just completed his studies, was selected by Martius for this project. He at once threw himself into the work with an enthusiasm which characterized him to the end of his busy life. The task of describing the Brazilian fish was completed and published in 1829. This was followed by research into the history of the fish found in Lake Neuchâtel. Enlarging his plans, in 1830 he issued a prospectus of a History of the Freshwater Fish of Central Europe. It was only in 1839, however, that the first part of this publication appeared, and it was completed in 1842.

In 1832 he was appointed professor of natural history in the University of Neuchâtel. The fossil fish there soon attracted his attention. The fossil-rich stones furnished by the slates of Glarus and the limestones of Monte Bolca were known at the time, but very little had been accomplished in the way of scientific study of them. Agassiz, as early as 1829, planned the publication of the work which, more than any other, laid the foundation of his worldwide fame. Five volumes of his Recherches sur les poissons fossiles ("Research on Fossil Fish") appeared at intervals from 1833 to 1843. They were magnificently illustrated, chiefly by Joseph Dinkel. In gathering materials for this work Agassiz visited the principal museums in Europe, and meeting Cuvier in Paris, he received much encouragement and assistance from him. They had known him for seven years at the time.

Before his first visit to England in 1834, the labours of Hugh Miller and other geologists brought to light the remarkable fish of the Old Red Sandstone of the northeast of Scotland. The strange forms of the Pterichthys, the Coccosteus and other genera were then made known to geologists for the first time. They were of intense interest to Agassiz, and formed the subject of a special monograph by him published in 1844–45: Monographie des poissons fossiles du Vieux Grès Rouge, ou Système Dévonien (Old Red Sandstone) des Îles Britanniques et de Russie ("Monograph on Fossil Fish of the Old Red Sandstone, or Devonian System of the British Isles and of Russia"). In the early stages of his career in Neuchatel, Agassiz also made a name for himself as a man who could run a scientific department well. Under his care, the University of Neuchâtel soon became a leading institution for scientific inquiry.

In 1837 Agassiz was the first to scientifically propose that the Earth had been subject to a past ice age, when he proposed to the Helvetic Society that ancient glaciers had not only flowed outward from the Alps, but that even larger glaciers had simultaneously encroached southward on the plains and mountains of Europe, Asia and North America, smothering the entire northern hemisphere in a prolonged Ice Age. In the same year, he was elected a foreign member of the Royal Swedish Academy of Sciences. Prior to this proposal, Goethe, de Saussure, Venetz, Jean de Charpentier, Karl Friedrich Schimper and others had made the glaciers of the Alps the subjects of special study, and Goethe, Charpentier as well as Schimper had even arrived at the conclusion that the erratic blocks of alpine rocks scattered over the slopes and summits of the Jura Mountains had been moved there by glaciers. The question having attracted the attention of Agassiz, he not only discussed it with Charpentier and Schimper and made successive journeys to the alpine regions in company with them, but he had a hut constructed upon one of the Aar Glaciers, which for a time he made his home, in order to investigate the structure and movements of the ice.

Thus familiarized with the phenomena associated with the movements of recent glaciers, Agassiz was prepared for a discovery which he made in 1840, in conjunction with william Buckland. The two visited the mountains of Scotland together, and found in different locations clear evidence of ancient glacial action. The discovery was announced to the Geological Society of London in successive communications. The mountainous districts of England, Wales, and Ireland were also considered to constitute centres for the dispersion of glacial debris; and Agassiz remarked "that great sheets of ice, resembling those now existing in Greenland, once covered all the countries in which unstratified gravel (boulder drift) is found; that this gravel was in general produced by the trituration of the sheets of ice upon the subjacent surface, etc."

In 1842–1846 he issued his Nomenclator Zoologicus, a Classified list, with references, of all names employed in zoology for genera and groups — a work of great labour and research. With the aid of a grant of money from the King of Prussia, Agassiz crossed the Atlantic in the autumn of 1846 with the twin purposes of investigating the natural history and geology of North America and delivering a course of 12 lectures on "The Plan of Creation as shown in the Animal Kingdom," by invitation from J. A. Lowell, at the Lowell Institute in Boston, Massachusetts. The financial offers presented to him in the United States induced him to settle there, where he remained to the end of his life. He was elected a Foreign Honorary Member of the American Academy of Arts and Sciences in 1846. Agassiz knew Harvard Botanist Asa Gray and they had a cordial relationship but disagreed on some scientific issues. For Example, Agassiz was a member of the Scientific Lazzaroni, a group of mostly physical Scientists who wanted American academia to mimic the autocratic academic structures of European universities, whereas Gray was a staunch opponent of that group. Agassiz also felt each human race had different origins but Gray believed in the unity of all humans.

He continued his lectures for the Lowell Institute. In succeeding years, he gave series of lectures on "Ichthyology" (1847–48 season), "Comparative Embryology" (1848–49), "Functions of Life in Lower Animals" (1850–51), "Natural History" (1853–54), "Methods of Study in Natural History" (1861–62), "Glaciers and the Ice Period" (1864–65), "Brazil" (1866–67) and "Deep Sea Dredging" (1869–70). In 1850 he married an American college Teacher, Elizabeth Cabot Cary, who later wrote introductory books about natural history and, after his death, a lengthy biography of her husband.

Agassiz served as a non-resident lecturer at Cornell University while also being on faculty at Harvard. In 1852 he accepted a medical professorship of comparative anatomy at Charlestown, Massachusetts, but he resigned in two years. From this time his scientific studies dropped off, but he was a profound influence on the American branches of his two fields, teaching decades worth of Future prominent Scientists, including Alpheus Hyatt, David Starr Jordan, Joel Asaph Allen, Joseph Le Conte, Ernest Ingersoll, william James, Nathaniel Shaler, Samuel Hubbard Scudder, Alpheus Packard, and his son Alexander Emanuel Agassiz, among others. He had a profound impact on Paleontologist Charles Doolittle Walcott and natural scientist Edward S. Morse. In return his name appears attached to several species, as well as here and there throughout the American landscape, notably Lake Agassiz, the Pleistocene precursor to Lake Winnipeg and the Red River, and Mount Agassiz, a bastion of the Palisade Crest, the largest glaciated region of California's Sierra Nevada.

During this time he grew in fame even in the public consciousness, becoming one of the best-known Scientists in the world. By 1857 he was so well-loved that his friend Henry Wadsworth Longfellow wrote "The fiftieth birthday of Agassiz" in his honor, and read it at a dinner given for Agassiz by the Saturday Club in Cambridge. His own writing continued with four (of a planned ten) volumes of Natural History of the United States which were published from 1857 to 1862. During this time he also published a catalog of papers in his field, Bibliographia Zoologiae et Geologiae, in four volumes between 1848 and 1854.

From his first marriage to Cecilie Bruan, Agassiz had two daughters in addition to son Alexander. In 1863, Agassiz's daughter Ida married Henry Lee Higginson, later to be founder of the Boston Symphony Orchestra and benefactor to Harvard University and other schools. On November 30, 1860, Agassiz's daughter Pauline was married to Quincy Adams Shaw (1825–1908), a wealthy Boston merchant and later benefactor to the Boston Museum of Fine Arts.

Agassiz is remembered today for his theories on ice ages, and for his resistance to Charles Darwin's theories on evolution, which he kept up his entire life. He died in Cambridge, Massachusetts in 1873 and was buried at Mount Auburn Cemetery, joined later by his wife. His monument is a boulder selected from the moraine of the glacier of the Aar near the site of the old Hôtel des Neuchâtelois, not far from the spot where his hut once stood; and the pine-trees that shelter his grave were sent from his old home in Switzerland.

Several animal species are named in honor of Louis Agassiz, including Apistogramma agassizi Steindachner, 1875 (Agassiz's dwarf cichlid); Isocapnia agassizi Ricker, 1943 (a stonefly); Publius agassizi (Kaup, 1871) (a passalid beetle); Xylocrius agassizi (LeConte, 1861) (a longhorn beetle); Exoprosopa agassizi Loew, 1869 (a bee fly); Chelonia agassizii Bocourt, 1868 (Galápagos green turtle); Philodryas agassizii (Jan, 1863) (a South American snake); and the most well-known, Gopherus agassizii (Cooper, 1863) (the desert tortoise).

Within his lifetime, Agassiz had developed a reputation for a particularly demanding teaching style. He would allegedly "lock a student up in a room full of turtle-shells, or lobster-shells, or oyster-shells, without a book or a word to help him, and not let him out till he had discovered all the truths which the objects contained." Two of Agassiz's most prominent students detailed their personal experiences under his tutelage, Samuel Hubbard Scudder in a short magazine article for Every Saturday and Nathaniel Southgate Shaler in his Autobiography. These and other recollections were collected and published by Lane Cooper in 1917, which Ezra Pound was to draw on for his anecdote of Agassiz and the sunfish.

In the 21st century, his resistance to Darwinian evolution, and the scientific racism evident in his writings on human polygenism, tarnished his reputation and led to controversies over his legacy.

An elementary school called the Agassiz Elementary School in Minneapolis, Minnesota existed from 1922-1981.

The Cambridge elementary school north of Harvard University was named in his honor and the surrounding neighborhood became known as "Agassiz" as a result. The school's name was changed to the Maria L. Baldwin School on May 21, 2002, due to concerns about Agassiz's racism, and to honor Maria Louise Baldwin the African-American principal of the school who served from 1889 until 1922. The neighborhood, however, continues to be known as Agassiz.

In 2005 the EGU Division on Cryospheric Sciences established the Louis Agassiz Medal, awarded to individuals in recognition of their outstanding scientific contribution to the study of the cryosphere on Earth or elsewhere in the solar system.

The accusations of racism have prompted the renaming of landmarks, schoolhouses, and other institutions which bear the name of Agassiz (which abound in Massachusetts). Opinions on these events are often mixed, given his extensive scientific legacy in other areas. In 2007 the Swiss government acknowledged the "racist thinking" of Agassiz but declined to rename the Agassizhorn summit. In 2017, the Swiss Alpine Club declined to revoke Agassiz's status as a member of honor, which he received in 1856 for his scientific work, because the club considered this status to have lapsed on Agassiz's death.

As Agassiz's descriptive work proceeded, it became obvious that it would over-tax his resources unless financial assistance could be found. The British Association came to his aid, and the Earl of Ellesmere—then Lord Francis Egerton—stepped in to help. The 1,290 original drawings made for the work were purchased by the Earl, and presented by him to the Geological Society of London. In 1836 the Wollaston Medal was awarded to Agassiz by the council of that society for his work on fossil ichthyology; and in 1838 he was elected a foreign member of the Royal Society. Meanwhile, invertebrate animals engaged his attention. In 1837 he issued the "Prodrome" of a monograph on the recent and fossil Echinodermata, the first part of which appeared in 1838; in 1839–40 he published two quarto volumes on the fossil Echinoderms of Switzerland; and in 1840–45 he issued his Études critiques sur les mollusques fossiles ("Critical Studies on Fossil Mollusks").