An enhanced water quality monitoring network was established in the A.R.M. Loxahatchee National Wildlife Refuge to complement existing monitoring. Data were collected from June 2004 through December 2005 at 53 sites, including 7 transects, and were analyzed to identify water management alternatives that minimize poor water quality and ecological impacts. We found 4 water quality zones, with a nutrient and mineral-impacted perimeter zone closest to canals and sources of poor quality inflow. Comparison of water quality patterns revealed that the relative difference between interior marsh and adjacent canal water levels was an important factor determining water movement and intrusion of canal water into the Refuge. The relative balance between overall water inflows to and outflows from the Refuge also was important, as was timing of inflows versus outflows. Preliminary water management recommendations include: limiting inflows to short durations when marsh and canal water levels are similar and interior depths are shallow; restricting duration of high inflows, as well as timing of inflows to occur when marsh water levels are significantly higher than canal water levels; discontinuing inflows when canal water levels are higher than marsh water levels; and timing inflows to coincide with outflows that are greater than inflows.