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This study describes the prevalent sedimentological and geochemical patterns and investigates the environmental status of the bottom of Gialova lagoon, a highly vulnerable coastal site of the EU's Natura 2000 network. For this task, lithological, geochemical, and microfaunal analyses of sediment samples were combined with a high-resolution bathymetric survey. Potential pollution was determined using geochemical-based (EF, I-geo, and PLI) and faunal (Foram-AMBI) indices. We find that sedimentation is mainly controlled by the bottom morphology, hydrodynamic variations, and biogenic productivity of the lagoon. The application of the multivariate factor analysis technique revealed four dominant factors explaining the geochemical processes occurring in the lagoon. The first factor, namely "terrigenous aluminosilicates associated with Corg vs. autochthonous biogenic carbonates", discriminates the deposition of detrital sediments, related to the high adsorption of heavy metals—versus bioclastic sediments. The "sulfides" factor represents an anoxic phase of the lagoon floor, whereas the "Mn-oxyhydroxides" factor indicates increased manganese content with several compounded trace elements. The "phosphate" factor reveals multiple sources of phosphorus in the lagoon. The lagoon bottom shows negligible to minor contamination in heavy metals, except Mo and Pb, which induce moderate pollution levels. The maximum contamination and environmental stress concern two small-sized, shallow basins within the lagoon. [ABSTRACT FROM AUTHOR]