Submerged large woody debris (LWD) in rivers and streams appears as spikes in bathymetry data collected at a decimeter resolution with a single-beam echo sounder. The LWD signal distorts any subsequent interpolation of bathymetry to an hydraulic model mesh or to a triangulated irregular network (TIN) for Geographical Information Systems (GIS). Two methods for separating the submerged LWD from the background bathymetry are investigated: 1) a new σ-discrimination method and 2) an adaptation of prior scale-space analysis techniques. The former is shown to effectively separate LWD from the background bathymetry. However, the latter is shown to be ineffective for this purpose. Separation of the background bathymetry and LWD signal allows the quantity and distribution of LWD to be separately mapped, providing a resource for biologists, geomorphologists and hydraulic engineers whose studies may be affected by the presence of LWD.