The Cienega de Santa Clara is a 5600 ha, anthropogenic wetland in the delta of the Colorado River in Mexico. It is the inadvertent creation of the disposal of brackish agricultural waste water from the U.S. into the intertidal zone of the river delta in Mexico, but has become an internationally important wetland for resident and migratory water birds. We used high resolution Quickbird and WorldView-2 images to produce seasonal vegetation maps of the Cienega before, during and after a test run of the Yuma Desalting Plant, which will remove water from the inflow stream and replace it with brine. We also used moderate resolution, 16-day composite NDVI imagery from the Moderate Resolution Imaging Spectrometer (MODIS) sensors on the Terra satellite to determine the main factors controlling green vegetation density over the years 2000–2011. The marsh is dominated by Typha domingensis Pers. with Phragmites australis (Cav.) Trin. Ex Steud. as a sub-dominant species in shallower marsh areas. The most important factor controlling vegetation density was fire. Spring fires in 2006 and 2011 were followed by much more rapid green-up of T. domingensis in late spring and 30% higher peak summer NDVI values compared to non-fire years (P < 0.001). Fires removed thatch and returned nutrients to the water, resulting in more vigorous vegetation growth compared to non-fire years. The second significant (P < 0.01) factor controlling NDVI was flow rate of agricultural drain water from the U.S. into the marsh. Reduced summer flows in 2001 due to canal repairs, and in 2010 during the YDP test run, produced the two lowest NDVI values of the time series from 2000 to 2011 (P < 0.05). Salinity is a further determinant of vegetation dynamics as determined by greenhouse experiments, but was nearly constant over the period 2000–2011, so it was not a significant variable in regression analyses. It is concluded that any reduction in inflow volumes will result in a linear decrease in green foliage density in the marsh.