Over the past years a continuously expanding list of ecological indicators termed "footprint" has been introduced to the scientific community, with the aim of assisting policy makers in better understanding the pressures that humanity places upon our planet. Nowadays footprint-type indicators have grown in interest and popularity, and the sustainability issues they are addressing have been far beyond the original scope. The mathematics behind the criterion of strong sustainability, for instance, has been demonstrated from the perspective of ecological footprint. As a consequence, accounting for natural capital use becomes one of the most compelling topics in the fields of footprint analysis. A three-dimensional (3D) model of the ecological footprint has been developed for the measurement of the human-induced natural capital use. This model is unique from other ecological footprint models in the sense that it allows, for the first time, a simultaneous assessment of the flows and stocks of natural capital at the regional and land levels. This paper starts from the idea of operationalizing the 3D model in a more accurate and robust way. To that end, we critically review the classical version of the 3D model, and propose to prevent unintended deficit shifting by tracking the appropriation of the capital flows and the depletion of the capital stocks among diverse types of land use. Using a revised version of the 3D model, the natural capital use for eleven nations throughout the world has been evaluated by means of three key indicators, namely the footprint size, the footprint depth, and the 3D footprint. It is indicated that over the past 10 years, a change has been witnessed with respect to international distribution of the appropriation of natural capital flows and of the depletion of natural capital stocks. In evaluating the spatial and temporal characteristics of natural capital use among these nations, four categories have been classified as follows: (1) double-high flows and stocks use category which is observed in US, France, and Germany (during the latter six years); (2) double-low flows and stocks use category observed only in India during the first two years; (3) the category with low flows appropriation and high stocks depletion observed in UK, Germany (during the first four years), Italy, Japan, India (during the latter eight years), and China; and (4) the category with high flows appropriation and low stocks depletion observed in Canada, Brazil, and Russia. Our findings suggest that the spatial distribution of national natural capital use is largely driven by not only natural resource endowment but also social and economic expansion. This is the reason why the intensity of natural capital use in developed nations in general is significantly higher than that in developing nations, even though the gap is narrowing. A negative correlation has been identified between the appropriation of flows and the depletion of stocks. More specifically, the resource-rich nations usually result in a high national footprint size per capita and a relatively low national footprint depth, while the resource-poor nations, on the contrary, have a low national footprint size per capita and a high national footprint depth. Our analysis implies that many industrial countries, in particular developing nations, follow the evolution process of natural capital use from low intensity to high intensity. The 3D ecological footprint model has the potential to uncover the link between human demand for natural capital and the process of national industrialization. Ultimately, this paper lays out some priorities for further improving natural capital assessment through the combination of footprint family and planetary boundaries under a multiregional input-output model.