This research aimed to determine the most effective methods to control Phragmites and restore native plant species. We took a large-scale approach to evaluate the effectiveness of two herbicides (glyphosate and imazapyr), and application timings (summer and fall), for controlling Phragmites to restore native plants and lost bird habitat. After three consecutive years of herbicide application, fall herbicide applications were superior to summer applications and no difference between the types of herbicide used was found. Even with effective control of Phragmites, important native plant recovery was slow and limited. In order to gain back the native plants that once dominated before Phragmites invaded, re-vegetation efforts such as seeding may be needed.