This thesis illustrates how geophysical and geochemical methods can be combined to study archaeological sites and obtain enhanced interpretations of the results using the complementary information they provide. Whilst these two disciplines tend to be used independently, this thesis brings them together, with a view to exploring their relationships and developing strategies that lead to non-destructive and cost-effective surveys. The investigation focuses on the correlation of geophysical and geochemical results over common archaeological features and their analysis using soil geochemistry in order to understand the factors of contrast involved in their detection. Five case study sites in Scotland were selected, each one presenting a specific challenge to be assessed by the integrated methodology developed in this thesis. The research employed a range of geophysical (earth resistance, magnetometry, magnetic susceptibility, FDEM and GPR) and geochemical (total phosphate and multi-element analysis) techniques routinely used in archaeological prospection. The different geophysical responses obtained over targeted archaeological features were considered with respect to soil texture, organic matter content, pH, conductivity and chemical composition from archaeological deposits, topsoil and subsoil samples. The results not only provide a nuanced understanding of the character of the archaeological features surveyed, but begin to develop a better insight of how the setting of a site may affect geophysical and geochemical datasets at Scottish archaeological sites. This thesis concludes that the detection of archaeological anomalies depends upon inter-related and site-specific contrast factors including: general site settings (e.g. the effect of highly variable glacial drift deposits), the type of features to be detected (e.g. cut or impervious), and the effect of soil post-depositional processes inside archaeological features and surrounding matrix. For example, at the prehistoric site at Forteviot site (Perthshire) redox processes inside archaeological ditches contribute to their negative magnetic response. Also, chemical composition related to anthropogenic organic materials may enhance the conductivity of theoretical impervious features as illustrated at the Bay of Skaill site (Orkney).