(1) Background: Leaf area index (LAI) is an essential structural property of plant canopies and is functionally related to fluxes of energy, water, carbon, and light in ecosystems; coupling the biosphere to the geo-, hydro-, and atmosphere. There is an increasing need for more accurate and traceable measurements among several spatial scales of investigation and modelling. We hypothesize that the spatial variability of LAI at the scale of crown sections of a single European beech (Fagus sylvatica L.) tree in a highly structured, mixed European beech-Norway spruce stand can be determined by simultaneous records of precipitation; (2) Methods: Spatially explicit measurements of throughfall were conducted repeatedly below beech and in forest gaps for rain events in leafed and in leafless periods. Subsequent analysis with a new regression approach resulted in estimating leaf and twig water storage capacities (SCleaf/twig) at point level independent of within-crown lateral flow mechanisms. Inverse modelling was used to estimate spatial litterfall (n = 99) distribution and litter production (mass, area, numbers) for single trees, as a function of diameter at breast height; (3) Results: As revealed by a linear mixed-effects model, SCleaf at the center of a beech canopies amounts to 4.9 mm in average and significantly decreases in the direction of the crown edges to an average value of 1.1 mm. Based on diameter-sensitive prediction of litter production, specific leaf area wetting capacity amounts to 0.260 l·m−2. A linear within-canopy dynamic of LAI was found with a mean of 17.6 m2·m−2 in the center and 4.0 m2·m−2 at the edges; and (4) Conclusions: The application of the method provided plausible results and can be extended to further throughfall datasets and tree species. Unravelling the causes and magnitude of spatial- and temporal heterogeneity of forest ecosystem properties contribute to overall progress in geosciences by improving the understanding how the biosphere relates to the hydro- and atmosphere.