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, who later founded the Boston Symphony Orchestra and was a benefactor to Harvard 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.

In the last years of his life, Agassiz worked to establish a permanent school where zoological science could be pursued amid the living subjects of its study.
In 1873, a private philanthropist (John Anderson) gave Agassiz the island of Penikese, in Buzzards Bay, Massachusetts (south of New Bedford), and presented him with $50,000 to permanently endow it as a practical school of natural science, especially devoted to the study of marine zoology.
The John Anderson school collapsed soon after Agassiz's death; it is considered a precursor of the Woods Hole Marine Biological Laboratory, which is nearby.

Agassiz had a profound influence on the American branches of his two fields, teaching many future scientists who would go on to prominence, including Alpheus Hyatt, David Starr Jordan, Joel Asaph Allen, Joseph Le Conte, Ernest Ingersoll, William James, Charles Sanders Peirce, 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.
Agassiz had a reputation for being a demanding teacher.
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: Scudder, in a short magazine article for Every Saturday, and 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 early 1840s, Agassiz named two fossil fish species after Mary Anning —Acrodus anningiae, and Belenostomus anningiae— and another after her friend, Elizabeth Philpot.
Anning was a paleontologist known around the world for important finds, but because of her gender, she was often not formally recognized for her work.
 Agassiz was grateful for the help the women gave him in examining fossil fish specimens during his visit to Lyme Regis in 1834.

Agassiz died in Cambridge, Massachusetts, in 1873 and was buried at Mount Auburn Cemetery, joined later by his wife.
His monument is a boulder from a glacial moraine of the Aar near the site of the old Hôtel des Neuchâtelois, not far from the spot where his hut once stood; his grave is sheltered by pine trees from his old home in Switzerland.

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

An ancient glacial lake that formed in the Great Lakes region of North America, Lake Agassiz, is named after him, as are Mount Agassiz in California's Palisades, Mount Agassiz, in the Uinta Mountains, Agassiz Peak in Arizona, and in his native Switzerland, the Agassizhorn in the Bernese Alps.
Agassiz Glacier (Montana) and Agassiz Creek in Glacier National Park and Agassiz Glacier (Alaska) in Saint Elias Mountains, Mount Agassiz in Bethlehem, New Hampshire in the White Mountains also bear his name.
 A crater on Mars Crater Agassiz
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, who later founded the Boston Symphony Orchestra and was a benefactor to Harvard 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.
In the last years of his life, Agassiz worked to establish a permanent school where zoological science could be pursued amid the living subjects of its study. In 1873, a private philanthropist (John Anderson) gave Agassiz the island of Penikese, in Buzzards Bay, Massachusetts (south of New Bedford), and presented him with $50,000 to permanently endow it as a practical school of natural science, especially devoted to the study of marine zoology. The John Anderson school collapsed soon after Agassiz's death; it is considered a precursor of the Woods Hole Marine Biological Laboratory, which is nearby.
Agassiz had a profound influence on the American branches of his two fields, teaching many future scientists who would go on to prominence, including Alpheus Hyatt, David Starr Jordan, Joel Asaph Allen, Joseph Le Conte, Ernest Ingersoll, William James, Charles Sanders Peirce, 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. Agassiz had a reputation for being a demanding teacher. 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: Scudder, in a short magazine article for Every Saturday, and 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 early 1840s, Agassiz named two fossil fish species after Mary Anning —Acrodus anningiae, and Belenostomus anningiae— and another after her friend, Elizabeth Philpot. Anning was a paleontologist known around the world for important finds, but because of her gender, she was often not formally recognized for her work.  Agassiz was grateful for the help the women gave him in examining fossil fish specimens during his visit to Lyme Regis in 1834.
Agassiz died in Cambridge, Massachusetts, in 1873 and was buried at Mount Auburn Cemetery, joined later by his wife. His monument is a boulder from a glacial moraine of the Aar near the site of the old Hôtel des Neuchâtelois, not far from the spot where his hut once stood; his grave is sheltered by pine trees from his old home in Switzerland.
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 involvement in scientific 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. An elementary school called the Agassiz Elementary School in Minneapolis, Minnesota, existed from 1922 to 1981.
An ancient glacial lake that formed in the Great Lakes region of North America, Lake Agassiz, is named after him, as are Mount Agassiz in California's Palisades, Mount Agassiz, in the Uinta Mountains, Agassiz Peak in Arizona, and in his native Switzerland, the Agassizhorn in the Bernese Alps. Agassiz Glacier (Montana) and Agassiz Creek in Glacier National Park and Agassiz Glacier (Alaska) in Saint Elias Mountains, Mount Agassiz in Bethlehem, New Hampshire in the White Mountains also bear his name.  A crater on Mars Crater Agassiz
Louis Agassiz