In Italy, the production of manila clams (Ruditapes philippinarum, Adams and Reeve, 1850) is mainly localized in northern Adriatic lagoons in the Po River delta, where shellfish farming provides important socio-economic revenue. However, in our globalized world, the seafood market is threated by fraudulent activities, in which agri-food products whose provenance is not certified are sold, posing a risk to consumer health. Multi-isotope ratio analysis is commonly used to trace the provenance of goods produced in different countries with different climatic and environmental conditions. Here, we investigated the reliability of this approach in terms of tracing the exact provenance of manila clams harvested in three Adriatic northern lagoons that are close to each other. We also verified the origin of samples bought at a local supermarket with a certificate of provenance. We carried out elemental analyses of carbon (C), nitrogen (N), and sulfur (S) and the respective isotopic ratios (13C/12C; 15N/14N; 34S/32S) on manila clam tissues, plus isotopic analyses of carbon (13C/12C), oxygen (18O/16O), and strontium (87Sr/86Sr) on manila clam shells. Each isotopic parameter can be used to identify the marine and continental contributions of water and/or nutrient supplies occurring in the lagoons. Therefore, the combination of isotopic parameters in a linear discriminant analysis (LDA) allowed for the identification of the lagoons in which the manila clams were produced.