This is an aquatic plant that grows entirely underwater. It has long intertwining stems with delicate feathery leaves about 1-2.5 cm long that are arranged alternately. The flowers are not in separate spikes but arise individually along the stem just above each leaf. The small hard fruits have vertical rows of small projections or thick hooks along the outside.

Leafy stems with mature fruit are needed for proper identification.

Positive identification for most water milfoil species (Myriophyllum spp.) requires fruit. When sterile, Myriophyllum farwellii is nearly impossible to separate from Myriophyllum heterophyllum unless turions are present. The fruits of Myriophyllum heterophyllum appear on very distinct stalks that stick above water, while Myriophyllum farwellii fruits appear on non-distinct submersed stems. Vegetative plants of Myriophyllum humile and Myriophyllum alterniflorum may also resemble Myriophyllum farwellii.