McDonald was appointed to an assistant position within the United States Fish Commission where he was a special agent under Baird and responsible for compiling and publishing fishery statistics related to the 1880 United States Census.
Following the census, he then served as superintendent of the shad hatcheries of the Potomac River.
During his subsequent years at the Fish Commission, McDonald was responsible for the distribution of "young fishes" and of "food-fishes" and later served as Chief of the Division of Fish Culture.
In 1885, McDonald was appointed Chief Assistant Commissioner of the Fish Commission.
He continued in that capacity until he was appointed by United States President Grover Cleveland in January 1888 to replace Dr. George Brown Goode as the Commissioner of Fish and Fisheries.
Brown had been temporarily filling the position of Fish Commissioner following Baird's death.
McDonald took his oath of office on February 18, 1888.
His appointment was widely recognized as an "excellent" choice due to the breadth of his experience, organizational and leadership abilities, and sense of duty and responsibility to the American people.
McDonald was also viewed as one of the "most accomplished" fish culturists in the United States at the time of his appointment.
As Fish Commissioner, McDonald was initially paid $5,000 per annum and had at his disposal three yachts and 22 fishing stations to conduct research and carry out the commission's efforts.

As Fish Commissioner, one of McDonald's most important works was his plan to undertake a biological and physical survey of American fisheries and fish culture more thorough than any previously undertaken.
McDonald believed the first step toward building "a comprehensive knowledge of the conditions of greatest productiveness" of American fisheries was to understand the primary food supply of fish, which McDonald termed "aquatic pastorage."
McDonald also initiated controversial changes in the Fish Commission imposing a bureaucratic structure inspired by his previous military career and solidifying the commission's emphasis on fish culture.

In 1893, McDonald warned Oregon governor Sylvester Pennoyer of "the disastrous outlook for the future of the salmon fisheries of the Columbia."
McDonald was appointed to an assistant position within the United States Fish Commission where he was a special agent under Baird and responsible for compiling and publishing fishery statistics related to the 1880 United States Census. Following the census, he then served as superintendent of the shad hatcheries of the Potomac River. During his subsequent years at the Fish Commission, McDonald was responsible for the distribution of "young fishes" and of "food-fishes" and later served as Chief of the Division of Fish Culture. In 1885, McDonald was appointed Chief Assistant Commissioner of the Fish Commission. He continued in that capacity until he was appointed by United States President Grover Cleveland in January 1888 to replace Dr. George Brown Goode as the Commissioner of Fish and Fisheries. Brown had been temporarily filling the position of Fish Commissioner following Baird's death. McDonald took his oath of office on February 18, 1888. His appointment was widely recognized as an "excellent" choice due to the breadth of his experience, organizational and leadership abilities, and sense of duty and responsibility to the American people. McDonald was also viewed as one of the "most accomplished" fish culturists in the United States at the time of his appointment. As Fish Commissioner, McDonald was initially paid $5,000 per annum and had at his disposal three yachts and 22 fishing stations to conduct research and carry out the commission's efforts.
As Fish Commissioner, one of McDonald's most important works was his plan to undertake a biological and physical survey of American fisheries and fish culture more thorough than any previously undertaken. McDonald believed the first step toward building "a comprehensive knowledge of the conditions of greatest productiveness" of American fisheries was to understand the primary food supply of fish, which McDonald termed "aquatic pastorage." McDonald also initiated controversial changes in the Fish Commission imposing a bureaucratic structure inspired by his previous military career and solidifying the commission's emphasis on fish culture.
In 1893, McDonald warned Oregon governor Sylvester Pennoyer of "the disastrous outlook for the future of the salmon fisheries of the Columbia."
Marshall McDonald