The objectives of this study were to estimate and evaluate potassium (K) and magnesium (Mg) budgets and flows of animal production in the basin of Dianchi Lake, China. Feed sampling and farmer interviews were conducted in field surveys. The supplies of K and Mg from local and external feeds and the retention, production and excretion of animals were calculated individually for dairy cows, fattening pigs, breeding sows, and broilers and laying hens. The K and Mg flows on a regional level were estimated using the individual budgets. At the individual level, in dairy cattle, the K and Mg supplied from local feeds accounted for large parts of the total nutrient intakes, whereas in the other animal categories most of the K and Mg in the feeds depended on external resources. Our findings also suggested that excessive Mg intake resulted in high Mg excretion and low use efficiency in dairy cattle and fattening pigs. At the regional level, the K and Mg amounts of manure produced and applied in the area (K: 339 and Mg: 143 t/year) exceeded those used as local feeds. Our results imply the animal production potentially increased the K and Mg loads in the regional agriculture system.