Evapotranspiration (ET) and other water balance components were estimated for Cienega de Santa Clara, an anthropogenic brackish wetland in the delta of the Colorado River in Mexico. The marsh is in the Biosphere Reserve of the Upper Gulf of California and Delta of the Colorado River, and supports a high abundance and diversity of wildlife. Over 95% of its water supply originates as agricultural drain water from the USA, sent for disposal in Mexico. This study was conducted from 2009 to 2011, before, during and after a trial run of the Yuma Desalting Plant in the USA, which will divert water from the wetland and replace it with brine from the desalting operation. The goal was to estimate the main components in the water budget to be used in creating management scenarios for this marsh. We used a remote sensing algorithm to estimate ET from meteorological data and Enhanced Vegetation Index values from the Moderate Resolution Imaging Spectrometer (MODIS) sensors on the Terra satellite. ET estimates from the MODIS method were then compared to results from a mass balance of water and salt inflows and outflows over the study period. By both methods, mean annual ET estimates ranged from 2.6 to 3.0 mm d⁻¹, or 50 to 60% of reference ET (ET_o). Water entered at a mean salinity of 2.6 g L⁻¹ TDS and mean salinity in the wetland was 3.73 g L⁻¹ TDS over the 33 month study period. Over an annual cycle, 54% of inflows supported ET while the rest exited the marsh as outflows; however, in winter when ET was low, up to 90% of the inflows exited the marsh. An analysis of ET estimates over the years 2000–2011 showed that annual ET was proportional to the volume of inflows, but was also markedly stimulated by fires. Spring fires in 2006 and 2011 burned off accumulated thatch, resulting in vigorous growth of new leaves and a 30% increase in peak summer ET compared to non-fire years. Following fires, peak summer ET estimates were equal to ET_o, while in non-fire years peak ET was equal to only one-half to two-thirds of ET_o. Over annual cycles, estimated ET was always lower than ET_o, because T. domingensis is dormant in winter and shades the water surface, reducing direct evaporation. Thus, ET of a Typha marsh is likely to be less than an open water surface under most conditions.