The technique of 13CH4 tracer injection through test limiters was applied to study the influence of surface roughness and substrate material on the local 13C deposition. Spherically shaped graphite limiters with integrated gas injection were prepared with two different grades of surface roughness, ∼0.1 and ∼1 µm. In addition, tungsten limiters with a roughness of ∼0.1 µm were used to study the substrate material effect. The limiters were exposed to the SOL plasma for two discharge scenarios, Ohmic and neutral beam heated. The 13C deposition efficiency—the ratio of the locally deposited to the injected amount of 13C—and the deposition pattern were evaluated by post-mortem surface analysis. Surface roughness has a pronounced effect and increases the 13C deposition efficiency on graphite with rougher surface by a factor of 3–5 compared with smoother graphite. On tungsten a factor of 2–4 less carbon is deposited than on graphite with similar surface roughness. A systematically higher amount of 13C (by a factor 1.5–2.5) was deposited on limiters exposed to Ohmic compared with neutral beam heated plasmas.