Mineral nutrient availability and in particular nitrogen abundance has a huge impact on plant fitness and yield, so that plants have developed sophisticated adaptive mechanisms to cope with environmental fluctuations. The vast natural variation existing among the individuals of a single species constitutes a great potential to decipher complex traits such as nutrient use efficiency. By using natural accessions of Arabidopsis thaliana that differ for their pattern of adaptation to nitrogen stress, we investigated the plant response to nitrate supplies ranging from 0.01 mM up to 50 mM nitrate. The biomass allocation and the different nitrogen pools in shoot and in roots were monitored to establish the nutrition status of each plant. Analysis of variation for these traits revealed genetic differences between accessions for their sensibility to nitrate availability and for their capacity to produce shoot biomass with the same nitrogen nutrition index. From the correlation matrix of all traits measured, a statistical model was formulated to predict the shoot projected area from the nitrate supply. The proposed model points out the importance of genetic variation with respect to the correlation between root thickness and amino acids content in roots. The model provides potential new targets in plant breeding for nitrogen use efficiency.