The impact of intensive aquaculture activities on marine sediments along three coastal areas in Greece was studied. The content of nine metals/metalloids (Cu, Cd, Pb, Hg, Ni, Fe, Mn, Zn, As), and three nutrients (P, N and C), that seem to accumulate in marine sediments, was determined under the fish cages (zero distance) and away (50 or 100 m) from them. Elevated concentrations for phosphorus, nitrogen, copper, zinc and cadmium were recorded in the areas where farming establishments are moored. In parallel, the intrinsic differences between the aquaculture facilities and their seasonal variations were investigated. The individual characteristics of each farm (local water currents, facilities' capacity, transferring mechanisms or the geological background) were the determinant factors. On the contrary, significant seasonal differences were not recorded. Statistical techniques, as the non-parametric Mann-Whitney U and Kruskal-Wallis tests and principal components analysis (PCA), factor analysis (FA) and discriminant analysis (DA), were used for the evaluation of the results. These chemometric tools succeeded to discriminate the sampling points according to their distance from the cages or the origin of the sample. Variables' significance, correlations and potential accumulation sources were also investigated.