Invasive species exert disproportionate impacts in wetlands and pose particular challenges for rare species persisting at small spatial scales. In the urbanized San Francisco Estuary (SFE), which contains 90% of California’s remaining coastal wetlands, invasive and rare species often co-occur. One narrow endemic taxon, the federally listed Suisun thistle (Cirsium hydrophilum var. hydrophilum) is restricted to two or three locations where the invasive perennial pepperweed (Lepidium latifolium) has an increasing presence. Perennial pepperweed has invaded salt, brackish, and freshwater wetlands around the SFE, leading to high management concern. In this study, we investigated how perennial pepperweed may contribute to further rarity of the Suisun thistle, by conducting a removal experiment and surveying soil-plant relationships. Removing pepperweed led to a doubling of native species relative cover and an increase in native species richness by an average of one species per plot, positive effects on Suisun thistle cover, number, and reproductive output, and shifts in soil properties. Combined with survey data inside and outside of pepperweed stands, we conclude that pepperweed competes with Suisun thistle via competition for space, nutrients, and light, interferes with the Suisun thistle’s reproductive success, and alters brackish marsh soil physicochemical characteristics to further favor pepperweed. We recommend local control of pepperweed to prevent further loss of Suisun thistle. Further, the wide range of mechanisms by which this invasion may proceed if unchecked should be considered in other settings where rare or uncommon species are at risk from invaders.