Desianti, N.; Potapova, M.; Enache, M.; Belton, T.J.; Velinsky, D.J.; Thomas, R., and Mead, J., 2017. Sediment diatoms as environmental indicators in New Jersey coastal lagoons. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay-Little Egg Harbor, New Jersey.The goal of this study was to explore the possible use of sediment diatoms as environmental indicators in New Jersey coastal lagoons. Diatom samples were collected from 100 sites in Barnegat Bay and Great Bay representing both subtidal and intertidal habitats. A total of 603 diatom taxa were found, with most samples characterized by high species diversity. A strong north-to-south salinity gradient in the study area was a major factor influencing composition of diatom assemblages. Subtidal sediments, especially in highly productive areas in the northern part of the Barnegat Bay, contained a high proportion of planktonic diatoms, especially small-celled Cyclotella and Chaetoceros species. Habitat type and physical properties, such as particle size and depth, were other important factors structuring diatom assemblages. Water-column nutrients and sediment contaminants did not show much effect on sediment diatoms, possibly due to the overriding effect of salinity or low variability in nutrient/contaminant concentrations. However, the organic matter content of sediments was significantly related to diatom species composition. Both sediment carbon and nitrogen were considerably higher in the northern part of the Barnegat Bay and other areas experiencing strong human impacts. This study developed diatom inference models for salinity and sediment nitrogen content and concluded that diatom species with relatively high optima for sediment nitrogen may be used as indicators of nutrient enrichment in studied lagoons.