Archaeological structures are commonly buried at shallow depths, nevertheless, their geophysical signatures measured at the surface may be weak and contaminated with noise, thus, difficult to interpret. However, regional-residual separation techniques commonly used in gravity and magnetics to enhance the signal of interest, also can be applied to the interpretation of one-dimensional resistivity profile data. Such a process is done based on a frequency analysis. The resistivity response of synthetic models has been computed analytically by the images method for a Wenner array. Different curves were analysed varying the observation step ( p ), the width ( t ) of two vertical layers, the resistivity (p) of the media, and the electrodes interval ( a ). The Fourier transform is applied to the theoretical resistivity profiles to compute and analyse its amplitude spectrum. Such a function presented three regions of interest. A low-frequency zone was selected to design a low-pass filter to calculate the “regional” of the resistivity curve. A “residual” resistivity anomaly was calculated by taking the difference between that and the observed profile. Such an anomaly depicted highs that corresponded to the location of the resistive interfaces. After assessing the technique with theoretical data, an application to a real case was studied. The real data are from the city of Denia (Alicante), located in the eastern coast of Spain, in the Mediterranean sea. The area of interest was covered by eight resistivity profiles. Two of them lay on a road under construction, where remains of a Roman structure were discovered during the construction works. Residual resistivity anomalies were computed by applying the method of regional-residual separation in the wave-number domain. A correlation process between the computed residual and the theoretical response of the “wall” model was carried out to locate the position of the boundaries of the village foundations. The geophysical interpretation enabled the archaeological work to discover the remains of a warehouse complex related to the ancient Roman port of Dianium, buried close to the surface below the road. So far no excavation has been undertaken in the reminder electrical profiles.