Aquatic plants are a critical component of the lake environment. Plants in lakes produce oxygen during photosynthesis, help stabilize shoreline and bottom sediments, and provide habitat and cover for fish and other aquatic inhabitants. The shallow water and soft sediments in Houghton Lake provide ideal conditions for aquatic plant growth and the lake supports a healthy and diverse population of aquatic plants. Over 25 plant species have been identified in Houghton Lake.
Since 2001, extensive vegetation surveys have been conducted on an annual basis to determine the type and distribution of plants in Houghton Lake. Of special concern is a plant called "Eurasian milfoil" (Myriophyllum spicatum). Eurasian milfoil is problematic in that it often establishes early in the growing season
and can grow at greater depths than most plants. Eurasian milfoil can proliferate and spread via vegetative propagation, in which small pieces break off, take root, and grow. It often forms a thick canopy at the lake surface that can seriously hinder recreational activity. Eurasian milfoil generally provides poor fish habitat when compared to native plant species. Once introduced into a lake, Eurasian milfoil may out-compete and displace more desirable plants and become the dominant species.
During the 1990s, Eurasian milfoil spread throughout much of Houghton Lake. By 2001, Eurasian milfoil infested nearly 11,000 acres of the lake and was common to dense in approximately 5,300 acres of the lake.