AbstractIn 2014, we mapped the complex landscape of component Area 5 at LdFa‐1, a 3000‐year‐old Palaeoeskimo site located in the deep interior of southern Baffin Island, using a combined magnetic and electromagnetic approach to define the physical characteristics of any large‐ or small‐scale anthropogenic anomalies. Measurements were made using a GEM Systems Overhauser magnetometer‐gradiometer and Geonics EM31 instrument, and a survey configuration designed to map in high resolution the total magnetic field, magnetic susceptibility and electrical conductivity responses of the underlying soils. Data‐reduction methods were used for each survey, including, for example, removal of temporal drift, to produce final responses related closely to the subsurface physical properties. Six geophysical responses are presented in the results: total magnetic field, vertical magnetic gradient, horizontal‐ and vertical‐dipole‐mode apparent susceptibility, and horizontal‐ and vertical‐dipole‐mode apparent conductivity. Spatial assemblages of small‐scale (<2 m) anomalies, correlated between the magnetic and magnetic susceptibility results and interpreted to be associated with groupings of igneous boulders in the shallow subsurface, define three areas of archaeological interest. One grouping is a roughly circular arrangement of anomalies with a diameter of 4 m. Its spatial correlation with a productive excavation unit at the site suggests an anthropogenic origin. The complementarity of data acquired at this site reduces the chances of misidentifying anomalies, for example, the apparent conductivity results support interpretation of larger‐scale anomalies observed at the site as being of lithogenic origin. This archaeogeophyiscal case study demonstrates the value of geophysical investigation in a complex Arctic archaeological environment and its role in providing information on subsurface archaeological features. Copyright © 2015 John Wiley & Sons, Ltd.