The Oliveri-Tindari Lagoon, located in North-Eastern Sicily (Italy) and composed of six lakes, is subject to continuous environmental changes. An integrated study focusing on sediment features and levels of contamination was carried out for three of the six lakes, which are of ancient origin: Verde, Mergolo della Tonnara and Marinello. A high primary production (26.89 μg l −1 ) was detected at Lake Verde; texture classification showed a typical grain size in the sediments of all lakes; the study of macronutrients highlighted 17.08 of total carbon in sediments from Lake Mergolo della Tonnara; toxic elements were detected at higher concentrations in the sediments of Lake Marinello in comparison to the others, while arsenic was found in high concentrations in all the samples tested, especially in Lake Verde, with a mean value of 17.25 mg kg −1 dry weight (d.w.). All the organic contaminants, except 4, 4′-dichlorodiphenyldichloroethylene, were below the detection limits in the sediments. Minimal microbiological contamination was found in both water and sediment samples. In the latter, we isolated several bacterial strains thriving in the presence of arsenic, which play a role in the biogeochemical cycle of arsenic. These preliminary results, obtained for the first time using a multidisciplinary approach, provide general information about the Oliveri-Tindari Lagoon area.