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Changes in land use and the development of coastal regions around the world have markedly increased rates of sediment input into estuarine and coastal habitats. Field studies looking at the consequences of terrestrial sediment deposition, water‐borne sediment, and long‐term changes in habitats indicate that increasing rates of sediment loading adversely affect the biodiversity and ecological value of estuarine and coastal ecosystems. Managing this threat requires means with which to convey the magnitude of the problem, forecast long‐term trends, and assess the risks associated with changes in land use. Here we focus on approaches for assessing the risks of changes in land use, which include combining biological effect studies with catchment and hydrodynamic modeling, using statistical models that forecast the distribution and abundance of species relative to changes in habitat type, and using sensitive …