The maternal diet and living environment can affect levels of chemical elements and fatty acid (FA) composition and their stable isotopes (δ13CFA) in human milk. Information obtained from questionnaires is frequently imprecise, thus limiting proper associations between external and internal exposures as well as health effects. In this study, we focused on seafood as a source of potentially toxic and essential elements and nutritional FAs. Concentrations of selected elements in human milk (As, Cd, Cu, Mn, Pb, Se and Zn) were determined using inductively coupled plasma mass spectrometry (ICP-MS) and Hg using cold vapour atomic-absorption spectrometry (CV-AAS). The identification and quantification of FAs in maternal milk were performed by an in-situ trans-esterification method (FAMEs), and the characterization of FAMEs was performed by gas chromatography with a flame ionisation detector (GC-FID). δ13CFA was determined by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). Seventy-four lactating Slovenian women from the coastal area of Koper (KP), with more frequent consumption of seafood, and the inland area of Pomurje (MS), with less frequent seafood consumption, were included in this study. Along with basic statistical analyses, data mining approaches (classification and clustering) were applied to investigate whether FA composition and δ13CFA could improve the information regarding dietary sources of potentially toxic elements. As and Hg levels in milk were found to be statistically higher in populations from KP than in those from MS, and 71% of individual FAs and 30% of individual δ13CFA values in milk differed statistically between the studied areas. In 19 cases, the levels of FAs in milk were higher in KP than in MS; these FAs include C20:5ω3 and C22:6ω3/C24:1ω9, which are typically contained in fish. In 16 cases, the mean percentage of FAs was higher in MS than in KP; these FAs include the PUFAs C18:2ω6, C18:3ω3, and C20:4ω6 which are important for human and infant growth. The difference in δ13C levels of C10:0, C12:0, C14:0, C16:1, C16:0, C18:1ω9c, C22:6ω3, and δ13C 18:0–16:0 in the study groups was statistically significant. In all seven cases where δ13C of FA significantly differed between KP and MS, δ13C was higher in KP, indicating a higher proportion of a marine-based diet. The data mining approaches confirmed that the percentage of selected FAs (iC17:0, C4:0, C18:2ω6t, aC17:0, CLA, and C22:4ω6) and δ13CFA of C18:1ω9c in human milk could be used to distinguish between high and low frequency of fresh seafood consumption.