The use of treated wastewater to restore freshwater inputs to arid and semi-arid wetlands is a relatively new concept, and the long-term effects of such practices on plant community structure are largely unknown. We compared vegetation composition, pore water salinity, and soil moisture along permanent transects at a restoration site receiving wastewater effluent since October 1998 to three nearby downstream sites subjected only to freshwater inputs via precipitation and river flooding. Local climate during this period was highly variable and included two droughts and a wet period that began with a series of large floods. Significantly lower pore water salinities were observed at the wastewater site compared to downstream sites, particularly during droughts, when salinities were 20‰–40‰ lower at the wastewater site. Between July 1997 and July 2002, cover of the clonal stress-tolerator, Salicornia virginica, decreased from 87% to 33% at the wastewater site, while cover of the clonal dominant, Borrichia frutescens, increased from 5% to 55%. In contrast, S. virginica cover increased at two downstream sites during the same period, while cover of B. frutescens remained relatively stable. Following large floods in summer 2002, which marked the beginning of a three year-wet period, B. frutescens cover increased at all sites. We concluded that constant wastewater additions and climate-driven wet periods affected plant community structure similarly by promoting expansion of the clonal dominant B. frutescens and inhibiting expansion of the stress-tolerant species S. virginica. We propose distinct management strategies for using wastewater to 1) increase plant cover, 2) promote endemic plant assemblages, and 3) maximize species richness.