This paper evaluates the total biomass and pools of major nutrients and ecologically important metals of the tree layer in the catchment of Plešné jezero (PL) in the Bohemian Forest (Šumava, Czech Republic), and compares them to analogous data on understory vegetation and soils. The results are based on field measurements and semi-automatic image analyses of aerial orthophotographs. The tree layer was relatively sparse with open canopy in some parts of the catchment. Stand density varied between 44 and 328 individuals per hectare. The catchment weighted mean total biomass of trees was 134 t ha−1 dry weight, of which needles, branches, roots, and stems represented 5%, 10%, 14%, and 71%, respectively. The stem wood and bark represented 67% and 4%, respectively, of the total tree biomass. The catchment weighted mean element pools were 568 and 3.0 mol m−2 (i.e., 68 and 0.42 t ha−1) for C and N, respectively. The other pools were 76 mmol P m−2, 602 mmol Ca m−2, 133 mmol Mg m−2, 39 mmol Na m−2, 347 mmol K m−2, 19 mmol Al m−2, 6.2 mmol Fe m−2, and 35 mmol Mn m−2. The element pools accumulated in the tree biomass represented from < 1% (Al, Fe) to 37% (C) of their total pools (soil + tree layer + understory vegetation) in the catchment. Pools of Ca and Mg in the tree biomass were similar to their exchangeable pools in the catchment soils, while those of K were 3 times higher. Nutrient (N, P, Ca, Mg, and K) and C pools in the tree biomass were 2–11 times higher than those in the understory vegetation, with the minimum for P and maximum for C.