Soil degradation assessments for mixed farming systems of the Molopo Basin (North West Province, South Africa and Southern District, Botswana) are provided from farmer–based research, designed to quantify nutrient fluxes across the farming system and to analyze the social, economic, political and environmental factors affecting nutrient management practices. This paper discusses the practical difficulties of how to use participatory farmer–led studies to assess soil degradation extent and its causes, and of then disseminating this information to farming communities and policymakers. Nutrient balance studies show that land degradation is evident on arable fields as soil nutrient depletion (the main threat to poorer manure–reliant farmers) and soil acidification (the main threat to wealthier farmers who have become dependent on inorganic fertilizer additions). Integrated nutrient management strategies involving both compound fertilizer additions and regular manure inputs can mitigate most soil degradation even on the sandy infertile Kalahari soils, but remain infrequently practised. The need to retain nutrient flows through the livestock sector from rangeland to arable land is thus vital to environmental sustainability and offers an applicable entry point for agricultural development initiatives and support. Factors identified as threatening the flow of nutrients from rangelands to arable lands include policy settings in terms of the different support programmes offered to communal farmers, village–level extension advice, household poverty levels and labour constraints.