The ability to model the suspended sediment flux (SSflux) and associated water flow from terrain affected by selective logging is important to the establishment of credible measures to improve the ecological sustainability of forestry practices. Recent appreciation of the impact of parameter uncertainty on the statistical credibility of complex models with little internal state validation supports the use of more parsimonious approaches such as data-based mechanistic (DBM) modelling. The DBM approach combines physically based understanding with model structure identification based on transfer functions and objective statistical inference. Within this study, these approaches have been newly applied to rainfall-SSflux response. The dynamics of the sediment system, together with the rainfall-river flow system, were monitored at five nested contributory areas within a 44 ha headwater region in Malaysian Borneo. The data series analysed covered a whole year at a 5 min resolution, and were collected during a period some five to six years after selective timber harvesting had ceased. Physically based and statistical interpretation of these data was possible given the wealth of contemporary and past hydrogeomorphic data collected within the same region. The results indicated that parsimonious, three-parameter models of rainfall-river flow and rainfall-SSflux for the whole catchment describe 80 and 90% of the variance, respectively, and that parameter changes between scales could be explained in physically meaningful terms. Indeed, the modelling indicated some new conceptual descriptions of the river flow and sediment-generation systems. An extreme rainstorm having a 10 to 20 year return period was present within the data series and was shown to generate new mass movements along the forestry roads that had a differential impact on the monitored contributory areas. Critically, this spatially discrete behaviour was captured by the modelling and may indicate the potential use of DBM approaches for (i) predicting the differential effect of alternative forestry practices, (ii) estimating uncertainty in the behaviour of ungauged areas and (iii) forecasting river flow and SSflux in terrain with temporal changes in rainfall regime and forestry impacts.