The concentrations of inorganic mercury (IHg) and methylmercury (MeHg) in surface sediments from the contaminated Aveiro Lagoon (Portugal) were determined by species-specific isotope dilution analysis. Different behaviour of IHg and MeHg was observed based upon multiple regression analysis, including geochemical characteristics of the surface sediments (fine fraction, concentrations of organic matter and metals) and non-Euclidean distances between sampling points. This data treatment method was valid over the entire concentration range of IHg and MeHg, allowing robust quantitative evaluation with respect to extrapolation. For IHg, there was statistical separation of the dispersion away from the contamination source and of Al concentration in the sediments. The MeHg concentrations followed those of IHg at high concentrations. The geochemical variables, such as concentrations of Ca (marine influence proxy), Mn and organic matter, were necessary to describe the behaviour of MeHg across the whole concentration range. The models for MeHg demonstrated that, close to the mouth of the lagoon, net production of MeHg was higher. In future, multiple regression analysis could be applied to separate and to evaluate quantitatively the effects of geochemistry and dispersion away from the contamination source in sediments contaminated with other substances.