Management at the Honouliuli and Waiawa Units of the Pearl Harbor NWR is similar to that conducted at the Ki‘i Unit of James Campbell NWR. The difference is that the wetlands at Pearl Harbor generally have higher salinity levels, which produce a different suite of plant species and require different levels of management effort. Emphasis, especially at Waiawa, is placed on the life history requirements of the endangered ae‘o. Water levels are manipulated to control the amount and location of mudflats, shallow and open water, and dry bare ground for foraging and nesting of endangered Hawaiian waterbirds, especially the ae‘o.
At the Kalealoa Unit management includes removal of invasive nonnative plant species and planting of native and endangered plant species, with an emphasis placed on the recovery of the endangered plant ‘Ewa hinahina (Achyranthes spledens var. rotundata). Also important at Kalealoa is the detection and restoration of anchialine pools, which are salt water pools in the raised limestone coral reef that are connected to the ocean via minute subterranean cracks and crevices within the coralline substrate. Restoration of these rare pools provides suitable habitat for several unique species including ‘ōpae‘ula, an imperiled native shrimp that requires these protected pools to survive.
Invasive tree removal at Kalealoa Unit also helps in the protection of historic World War II artifacts.