Past waterway management practices worldwide involved extensive removal of instream woody habitat (IWH) and riparian vegetation. The importance of instream woody habitat for healthy aquatic ecosystems has now been recognised, with management approaches reversed to reintroduce instream woody habitat and replant riverbanks. Knowledge of natural or pre-disturbance IWH loads is useful to guide such restoration programs; however, such datasets are often unavailable. In this study, natural IWH loads were mapped along 105 km of undisturbed rivers in south-eastern Australia. This field dataset was modelled, using boosted regression trees, against geomorphic, environmental and climatic variables to predict natural IWH loads in rivers across Victoria. Mapped natural IWH loads averaged 0.029 m3 m–2 (±0.005), ranging from 0.083 to 0.002 m3 m–2. Natural IWH volumes were predicted to range from 0 to 0.102 m3 m–2. Distinct IWH loading trends were noticeable over larger spatial scales. Eastern Victoria showed relatively lower natural IWH loads than did western Victoria. Because many stream restoration efforts do not have a quantifiable knowledge of natural IWH load, the results of the present study provide some guidance. The predicted IWH loadings are a useful first step in identifying broad areas for further investigation and a natural condition base for current IWH condition modelling.