Invasive species have the potential to create positive feedbacks and push an ecosystem into an alternative state through a variety of mechanisms. Unless the drivers behind these feedbacks are understood, restoring a system to a more desirable state may not be possible. We used a long-term vernal pool restoration project based out of Travis Airforce Base, Fairfield, CA, U.S.A. to examine natural pools dominated by either invasive or native plant communities, and restored pools predominately composed of invasive plants. We determined that plant community structure is drastically altered towards invasive grasses with the addition of a single centimeter of litter. In the absence of this litter layer, community structure was driven by a non-native forb rather than native species. We also found that native plant-dominated vernal pools have a longer inundation duration and are deeper compared to invasive-dominated pools, regardless of construction status. These results suggest that once invasive grasses establish through lower inundation depths, their litter deposition can initiate a positive feedback to maintain an invasive alternative state. However, even after litter removal, non-native forbs can replace the grasses causing a second alternative state still separate from the most desirable native dominated state. This study directly demonstrates that invasive species, and their positive feedbacks, may limit the success of ecological restoration. To effectively restore a system all constraints must be identified and removed before successful restoration can occur.