Balancing nutrient inputs and exports is essential to maintaining soil fertility in rainfed crop and pasture farming systems. Soil nutrient balances of land used for crop and pasture production in the south-west of Western Australia were assessed through survey data comprising biophysical measurements and farm management records (2010–15) across 184 fields spanning 14 Mha. Key findings were that nitrogen (N) inputs via fertiliser or biological N2 fixation in 60% of fields, and potassium (K) inputs in 90% of fields, were inadequate to balance exports despite increases in fertiliser usage and adjustments to fertiliser inputs based on rotations. Phosphorus (P) and sulfur (S) balances were positive in most fields, with only 5% returning losses >5 kg P or 7 kg S/ha. Within each of the three agroecological zones of the survey, fields that had two legume crops (or pastures) in 5 years (i.e. 40% legumes) maintained a positive N balance. At the mean legume inclusion rate observed of 20% a positive partial N budget was still observed for the Northern Agricultural Region (NAR) of 2.8 kg N/ha.year, whereas balances were negative within the Central Agricultural Region (CAR) by 7.0 kg N/ha.year, and the Southern Agricultural Region (SAR) by 15.5 kg N/ha.year. Hence, N budgets in the CAR and SAR were negative by the amount of N removed in ~0.5 t wheat grain, and continuation of current practices in CAR and SAR fields will lead to declining soil fertility. Maintenance of N in the NAR was achieved by using amounts of fertiliser N similar to other regions while harvesting less grain. The ratio of fertiliser N to legume-fixed N added to the soil in the NAR was twice that of the other regions. Across all regions, the ratio of fertiliser N to legume-fixed N added to the soil averaged ~4.0:1, a major change from earlier estimates in this region of 1:20 under ley farming systems. The low contribution of legume N was due to the decline in legume inclusion rate (now 20%), the low legume content in pastures, particularly in the NAR, and improved harvest index of lupin (Lupinus angustifolius), the most frequently grown grain legume species. Further quantifications of the effects of changing farming systems on nutrient balances are required to assess the balances more accurately, thereby ensuring that soil fertility is maintained, especially because systems have altered towards more intensive cropping with reduced legume production.