A systems analysis approach was used to assess farm-scale nutrient and trace element sustainability by combining full-scale field experiments with specific studies of nutrient release from mineral weathering and trace-element cycling. At the Öjebyn dairy farm in northern Sweden, a farm-scale case study including phosphorus (P), potassium (K), and zinc (Zn) was run to compare organic and conventional agricultural management practices. By combining different element-balance approaches (at farm-gate, barn, and field scales) and further adapting these to the FARMFLOW model, we were able to combine mass flows and pools within the subsystems and establish links between subsystems in order to make farm-scale predictions. It was found that internal element flows on the farm are large and that there are farm internal sources (Zn) and loss terms (K). The approaches developed and tested at the Öjebyn farm are promising and considered generally adaptable to any farm.