Lagoa Salgada is located in the northern coast of Rio de Janeiro and is of great scientific relevance for its modern stromatolites. This study aimed to map the types of microbialites, identify damage and threats and provide geoconservation suggestions. Microbialite mapping and sampling was authorized by the administrative body of the Lagoa do Açu State Park - PELAG, where the lagoon is partially located. Petrographic analysis was conducted on stromatolite types according to external morphology. Geology and heritage value data were added to the GEOSSIT platform and analysis of ecosystem services and scientific value was performed based on bibliometrics. Three types of stromatolite were distinguished and mapped (large domal, small domal and branched columnar) with two types of microbial mat (colloform and polygonal). These morphologies suggest different hydrodynamic agents in the growth process and regarding the position in the water column. According to GEOSSIT criteria the site stands out as a “Geosite of International Relevance” and of national scientific relevance for education and tourism, serving as a model for studies on preterit environments. Ecosystem services provided by its Geodiversity, are: (a) Regulation: atmospheric processes related to photosynthesis performed by bacteria during the carbon cycle, fixing carbonates in the biostructures; (b) Support: provision of a habitat established by the seasonal hyper-salinity of the environment; (c) Provision: presence of ichnofossils and considered an environment analogous to the Pre-Salt rock reservoir; (d) Culture: environmental quality of the landscape; geotourism through a Geological Pathways Project panel; historical significance (Roteiro dos Sete Capitães); inspiration for poems and legend; and a location for didactic excursions; and (e) Knowledge: history of the evolution of life on Earth; the first Holocene stromatolites in Brazil; study of sea-level variation; and the possibility of generating jobs in Geoparks. Regarding the scientific value, 32 citations were found in the bibliography among complete articles in periodicals, theses, dissertations, monographs and book chapters. Damage and threats to which the stromatolites are subjected were identified. GEOSSIT recommends medium-term protection. Anthropic remobilization of the biostructures, agricultural use, proximity to the Açu Port Complex and non-inclusion of the lagoon’s northern portion in the PELAG area, despite being the only area with branched stromatolites, can be highlighted as damage and threats. Promotion through lectures, booklets, field classes, and maintenance of the Geological Pathways Panel aimed at the local population and visitors is necessary. Scientific knowledge should be incorporated into management of the Geosite to achieve Geoconservation.