The efficient use of agricultural water and nitrogen fertilizer is necessary due to the increase in food demand and water scarcity. The application of biochar in this context has been suggested as a beneficial strategy. The objective of this study was to evaluate the effects of single application of natural nanobiochar to the soil on soil aggregation, and on mitigating the negative effects of different deficit irrigation intensities and low nitrogen fertigation condition on broccoli plant performance properties. In the present study, the effects of single application of natural nanobiochar (0 and 10% by weight), on soil aggregation, as indicated by the mean weight diameter of water-stable aggregates were investigated. Additionally, the efficacy of natural nanobiochar in ameliorating the deleterious effects of deficit irrigation (at levels of 100, 75, and 50% of full irrigation) and nitrogen fertigation (at rates of 225 and 300 kg N ha−1) on the performance traits of broccoli plant were assessed. This investigation was conducted over a two-year period using a porous clay pitcher sub-surface irrigation. Natural nanobiochar addition improved the soil structure (i.e., mean weight diameter). Plants grown in unamended soils subjected to deficit irrigation and low nitrogen conditions exhibited significant decrease in the photosynthetic rate, stomatal conductance, head density, fresh and dry head weights, stem diameter, nutrients concentrations, total chlorophyll, chlorophyll a, chlorophyll b contents, while increasing proline contents, carotenoids contents and ion leakage. Addition of natural nanobiochar to soil improved the photosynthetic rate, stomatal conductance, head density, head fresh and dry weights, stem diameter, nutrient concentrations, total chlorophyll, chlorophyll a and chlorophyll b contents. Furthermore, the proline contents, carotenoids content and ion leakage of plants were significantly reduced under the deficit irrigation and nitrogen fertigation conditions. Hence, it is deduced that natural nanobiochar not only can improve soil structure but also attenuates water and nitrogen consumption, with minor detrimental impacts on crop yield.