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Floodplains are critically important ecosystems that provide a whole suite of ecosystem services, including nutrient and carbon sequestration, flood mitigation, water storage, and critical wildlife habitat. However, human modification of rivers and floodplains through channelization, artificial levee construction, reductions in the active floodplain area, and water management can significantly reduce the ecosystem function of river–floodplain systems. In this study, we evaluated the changes in the nutrient loading of the Kissimmee River floodplain during the restoration of the river–floodplain system. In addition to time-series loading analysis, we also evaluated soil nutrient concentrations across the lower portion of the Kissimmee River floodplain. During the 44-year nutrient loading time-series, the floodplain remained a nutrient exporter with changes in nutrient loading generally corresponding to both water quality (i.e., point source reductions) and hydrologic restoration activities in the watershed and Kissimmee River floodplain. During the study period, inputs of total phosphorus and total nitrogen loads from upstream either significantly increased or remained the same. In addition to external sources of nutrients, internal sources of nutrients from floodplain soils can also contribute to the total nutrient export from the system. These internal sources could be organic via the decomposition of organic matter or geologic from the original excavation of the canal and/or restoration backfilling. Soil nutrient concentrations vary between vegetative communities and landscape position and could be a significant source of phosphorus to the downstream system, which is plagued by eutrophic conditions. Therefore, as floodplain function in the Kissimmee River continues to be restored and managed, additional effort may be needed to address nutrient inputs and internal legacy nutrients. Full article