Syngnathids are considered flagship species of estuarine and coastal environments. However, most of the Mediterranean species are still classified as data-deficient (DD) at a global level according to the IUCN Red List of Threatened Species. In central Italy, several areas host potentially suitable habitats for syngnathids but have not been previously reported in the literature; the estimation of population parameters and habitat partitioning at these sites may help to assess their conservation status. In this study, we investigated the abundance, distribution, and habitat preferences of sympatric populations of Hippocampus hippocampus, H. guttulatus, Syngnathus abaster, and Nerophis ophidion in Sabaudia Lake (Tyrrhenian Sea, Italy). While confirming the primary importance of a healthy coastal habitat, we retrieved hints about species ecology and habitat use. The species distribution in the study area highlights the role of habitat complexity in supporting local populations of these sensitive species.