Unfortunately, many plants found in the park are invading the native ecosystem, choking out the native vegetation and damaging archeological sites. The park is battling these alien invaders with pesticides, vegetation removal and out-planting native species.

In recent years non-native red mangrove has aggressively invaded many shoreline habitats in Hawai'i.  Beginning in the mid-70s, red mangrove overran both Kaloko and Aimamkapa Ponds.  Shortly after the park acquired the lands the park staff aggressively removed the mangrove.  This was a huge undertaking and the park's example has now been widely copied on the other islands in Hawai'i.  Red mangrove has been entirely removed from the park - but the management staff constantly monitors and removes all new seedlings of this invasive weed.