Research for nutrient optimization and crop nutrient use efficiency requires precise control on soil nutrient status. While nutrient-depleted soils are preferable to artificial soils or hydroponics, reliable and affordable methods for nutrient removal are lacking. We report the systematic standardization and validation of a simple method to wash soil with purified deionized water for the removal of nutrients such as nitrogen (N), phosphorus (P), potassium (K), calcium (Ca) and organic carbon. Sandy soil was washed with RO water (1:1, w/v) followed by several washes with Type 1 ultrapure water (2:1, w/v) and tested after each wash for the removal of organic carbon, N, P, K, and Ca. After seven washes, total dissolved solids (TDS) were reduced to 5 ppm, conductivity to 10 µS, organic carbon content was reduced by 78%, while N by 19.5%, P by 30%, K by 48% and Ca by 29%. Two genotypes of rice were grown for full life cycle under normal and low N fertilizer (urea) levels to demonstrate that soil depleted with nutrients by our method supports normal plant growth in the greenhouse and allows experiments impossible under field conditions. Precise control on the nutrient status of the soil by our method also helped demonstrate yield differences between genotypes and N regimes and also that higher grain yields can be obtained with low nitrogen (N) input. Thus, our method facilitates better design of experiments for precise determination of nutrient requirements for crop growth and nutrient use efficiency.