Broad infestations of invasive, non-native vegetation have transformed wetlands around the world. Ludwigia hexapetala is a widespread, amphibious invasive plant with a creeping growth habit in open water and an erect growth habit in terrestrial habitats. In the upper San Francisco Estuary of California, L. hexapetala is increasingly terrestrializing into marshes and this expansion may be facilitated by allelopathy. We conducted the first field-based study on L. hexapetala allelopathy to determine whether (1) three allelochemicals known to be exuded by L. hexapetala are expressed in situ, (2) the allelochemicals are detectable in leaves, soil, and water, and (3) allelopathic expression varies by season, salinity, and growth habit (open water “patch” vs. terrestrial marsh “interface” locations). Water, soil, and L. hexapetala leaves were collected in two freshwater sites and two oligohaline sites in the upper San Francisco Estuary in summer 2021, fall 2021, and spring 2022. Myricitrin and quercitrin, known allelochemicals, and salipurposid, a newly identified polyphenol, were detected in water, soil, and leaves. There were significant differences in allelochemical concentrations under fresh versus oligohaline conditions in water and soil, but not leaves. All three allelochemicals generally had higher concentrations in patch versus interface locations, suggesting that L. hexapetala allelopathy plays a greater competitive role in open water than terrestrial habitats. Leaf concentrations of each allelochemical varied seasonally; however, both myricitrin and salipurposid had heightened concentrations in spring. These results suggest that herbicide application in early spring may be most effective in controlling L. hexapetala terrestrialization from open water to marshes.