We surveyed in detail the Chalcolithic lithic workshop Fofanovo XIII an East Fennoscandian region by ground-penetrating radar (GPR). A high-frequency antenna unit was applied to map small-scale features, mainly waste flakes. To substantiate the efficiency of the GPR technique, we performed a primary analysis of a set of equivalent models in a sandbox. The laboratory-scale GPR investigation highlights differences in GPR patterns depending on the spatial arrangement of small features and supports the further interpretation of real-life data. The GPR survey in the field covered 2200 m2, revealing areas with a high density of artefacts in the cultural layer and locating individual structural elements of the Fofanovo XIII archaeological site. We suggested using microdebitage samples from manual probing to verify the detected anomalous values of GPR attributes. The results point to a significant correlation between microdebitage and the envelope peak amplitude of the echo signal. Ultimately, our study confirmed the cultural layer in the Fofanovo XIII workshop site to be rich in lithic production wastes, indicating it was a place of mass-scale production of lithic chopping tools.