Three irrigation canals provide life-giving water to Topock Marsh and staff members control and monitor water levels to provide habitat for a myriad of species that utilize the area. Water from the Colorado River is also used to maintain the four moist soil units and four agricultural fields in Pintail Slough. The same water is used to promote the growth of native trees in the Beal restoration area, encourage mesquite tree growth in re-vegetated areas, and water the agricultural fields to provide food for birds.

Refuge employees are constantly battling invasive species, such as salt cedar, that can have negative impacts on native plant and wildlife communities. Salt cedars have a long tap root that reachs the water table with ease and outcompetes native trees for available groundwater. Salt cedar also prevents other plants from establishing because they precipitate salt, which deposits on the surface of the soil.  Without repeated flooding, soil salinity can become too high for native plants to establish and grow.  Although salt cedar does provide breeding habitat for a few species of birds and shade to small mammals, it is not suitable for forage. The refuge works diligently to prevent salt cedar from re-sprouting in previously treated areas and the soil is watered to leach the salt from areas where salt cedars have been removed. Once the soil is leached, native trees such as screwbean and honey mesquite are planted. In this way, areas that were previously dominated by salt cedar are converted back to landscapes where native plants take root once again and provide important habitat for native wildlife to rest, nest and feed.