Lagoons are the hotspot ecosystems whose sustainability should be secured using the ecological assessment indicators. This study aimed to quantify the surface sediment metal distributions of cardak Lagoon in the Marmara region of Turkey, to characterize their natural and anthropogenic sources and transport mechanisms and to assess their potential ecological risks. The surface sediment samples were collected from 11 stations using Van Veen grab, while for the background values to be determined, core sampling was used from two stations. The analyses of multiple elements, total organic carbon, carbonate, and chlorophyll degradation by-products were carried out to characterize sediments. Enrichment factor and the indices of potential ecological and toxic risks were applied to assess the ecological status of the surface sediments. The operation of the gold mine in the close vicinity was found to be responsible for the enrichment of Au and Hg in the lagoon sediments. Cd, Tl, Sb, and Sr were the other elements responsible for the enrichment. The potential risk levels of the lagoon varied between the low and significant levels. The riskiest elements were found to be Hg and Cd which in turn pointed to the mining and agricultural activities as the most dominant human disturbance. The toxic risk index of cardak Lagoon was estimated to range from 5.21 to 11.00, with a low mean value of 7.98. The C:N ratio range of 8.52 to 134.93 (a mean of 29.07) indicated that the organic C source was mostly of the terrestrial origin, in particular, from the surrounding agricultural lands.