In an effort to provide the greatest diversity of habitats, management activities primarily focus on water, grasslands, exotic species and public use. The refuge's recreated wetlands consist of diked pools of water. Water levels are manipulated in the refuge pools to create conditions that provide a mix of underwater plants, emergent vegetation, and open water. Summer or winter drawdowns (draining), gradual drawdowns and stress flooding are all water management regimes used at Montezuma National Wildlife Refuge.
The goals of the refuge's grassland management program are to; 1) provide a diversity of field types, 2) reduce the encroachment of woody shrubs, and 3) encourage the growth of a variety of grasses. Common grassland management techniques include periodic mowing, prescribed burning and planting.

Numerous exotic species are found at Montezuma. Purple loosestrife is the exotic species that has had the greatest impact on the quality of habitats available at Montezuma. Current management of purple loosestrife primarily involves the use of biological control agents, weevils and beetles that are host-specific (feed and live exclusively on purple loosestrife). The goal of this biological control program is to establish the competitive balance between native plant species and purple loosestrife.

The public use program at Montezuma provides wildlife oriented educational and recreational opportunities compatible with refuge management objectives. Public use facilities and programs include the 3.5-mile Wildlife Drive, 2-mile Esker Brook Trail, .75-mile South Spring Pool Trail, Visitor Center, observation towers and platforms, fishing access sites, hunting programs, trapping program, educational programs and materials, guided tours and special programs. Exhibits, brochures, kiosks and programs are used to convey information to the public about the management activities and programs of the refuge as well as those of the Fish and Wildlife Service.