Herbicides are a critical tool for controlling aggressive invasive species, especially during large-scale restoration efforts, but their persistence in soils can hinder the establishment and success of desirable vegetation. Soil residence times differ among herbicides, and plant species exhibit variable tolerance to residues, causing difficulty in determining appropriate timelines for revegetation activities following herbicide application. Imazapyr is a herbicide commonly used to control highly aggressive species such as giant reed (Arundo donax L.), with reported soil residence time ranging from 3 to 12 mo. However, we observed herbicide damage on foundational tree species installed more than 2 yr after imazapyr was applied to control expansive A. donax monocultures as part of a large-scale riparian forest restoration project. We monitored signs of herbicide damage and growth for willow (Salix) and cottonwood (Populus spp.) individuals installed from cuttings to evaluate the relative susceptibility to and differential impacts of imazapyr residues on trees established using this standard propagation technique. Individuals from all species exhibited signs of herbicide damage, and the height of damaged individuals was significantly lower than that of healthy individuals across species. Red willow (Salix laevigata Bebb) had the greatest percentage of damaged individuals (27%), but the smallest reduction in height due to herbicide damage (−13%). The frequency of herbicide damage was similar among Populus species (≤13%), but the fastest-growing species, black cottonwood (Populus trichocarpa Torr. & A. Gray), experienced a much greater decline in growth (−67%) compared with Fremont cottonwood (Populus fremontii S. Watson) (−32%) and Fremont × black cottonwood (P. × parryi Sarg.) (−31%). The study found that imazapyr, when used to control invasive monocultural species, can have lingering, previously undocumented effects on non-target riparian vegetation. Despite these negative impacts, imazapyr is still one of the most effective treatment options for some aggressive invaders. Thus, practitioners should be aware of the potential long-term effects of imazapyr and carefully consider species selection and planting schedule during revegetation.