There are currently several weed species found within the area. Juncus planifolius, Cyperus halpan, Holcus lanatus, and Hypochoeris radicata are the most commonly encountered species within Hanawi NAR. Habitat altering species such as Tibouchina herbacea, Rubus argutus, and kahili ginger (Hedychium gardnerianum) are found occasionally or are present in small numbers. Although the primary dispersal mechanism for each of these species is not well documented, it is assumed that many of these weeds are dispersed by human, ungulate, and forest bird activity.

The research and management efforts of the Maui Forest Bird Recovery Project require a substantial human presence within Hanawi NAR. As a result, there is a considerable potential for the introduction and spread of weed species as a result of human activity. Introduction of aggressive weeds such as kahili ginger or miconia have proven to be devastating to native rainforest ecosystems in Hawaii. Fortunately, these species have not yet reached the upper, fenced units of Hanawi.

In order to limit the dispersal and establishment of weed populations, a systematic and aggressive program of monitoring and control has been implemented. The MFBRP documents the location of all non-natives encountered in the field and weed control is necessary to limit the spread of existing populations and to prevent the establishment of new ones. Control efforts are focused on ecosystem modifying species and incipient populations that can be controlled through minimal effort. Non-native plants in camp areas, landing zones, main trails, and along fence lines are also a high priority for control in order to prevent their spread into more remote areas of Hanawi NAR. Because invasive plants are often very difficult to control once they have entered an area, prevention of new introductions is crucial.

In order to maintain the pristine ecosystem within Hanawi, the MFBRP adheres to a strict alien prevention protocol. Before each field trip, all gear is thoroughly inspected and cleaned. All dirt, seeds, and insects are carefully removed. Project field gear is never taken off island or into other less pristine areas of Maui. Within Hanawi, crew members do not hike upslope from weed infested areas into more pristine areas. Such steps are essential to maintain a suitable habitat for the last of Hawaii's native forest birds.