The Loxahatchee National Wildlife Refuge (Refuge) developed as a system with waters low in nutrients. Today, the Refuge wetlands are impacted by inflows containing elevated nutrient concentrations originating from agricultural sources. We analyzed water quality sampled at 54 sites in the Refuge. The Refuge was divided into northern, central, and southern latitudinal areas and then perimeter, transition, and the interior zones based on distance from the canal towards the Refuge interior. In the perimeter zone, total dissolved solids (TDS), silicon (Si), and total phosphorus (TP) concentrations in water were higher in the northern than the central area and TDS, Si, SO4, and TP concentrations in water were higher in the central than the southern area. In general TDS, Ca, Cl, Si, SO4, and TP loads in the northern perimeter, transition, and interior zones decreased from 2005 to 2009. The decrease is less pronounced in the central and southern areas than the northern area. As water flowed southward for over 30 km from the northern to the southern area in the perimeter zone, most water quality parameters analyzed were reduced in the water column. However, large amounts of Ca and Cl were added to the water column indicating that canal water is continually diffusing and intruding into the Refuge in all zones. In the perimeter zone, and to a lesser degree in the transition zone, the Refuge has accumulated substantial amounts of Ca, Si, SO4, and TP in vegetation and soils during the sampling period.