The data herein were used to assess the importance of geogenic-derived nutrients on long-term forest ecosystem nutrition in two mountainous temperate forest ecosystems in southern Germany (Conventwald/Black Forest and Mitterfels/Bavarian Forest). Presented are element concentrations of various forest ecosystem compartments along with the soil pH, chemical depletion fractions (CDF), mass transfer coefficients (τ_(X_i)^X), radiogenic Sr isotope ratio (87Sr/86Sr) of soil and saprolite as well as in situ 10Be concentrations of bedload sediment. Element concentrations measured by X-ray fluorescence (XRF) are provided for drilling core samples (depth: 20 m, site Conventwald (CON), and 30 m, site Mitterfels (MIT)) including unweathered parent bedrock (paragneiss) and regolith comprising soil, saprolite and weathered bedrock but also for bedload sediment. Element concentrations were also measured by ICP-OES to determine the element composition of the soil´s and saprolite´s water-soluble, easily exchangeable, carbonate and organic-bound fraction. In addition, ICP-OES derived element concentrations are reported for plant tissues such as needles, leaves, and stem wood comprising heartwood (dead part of wood) and sapwood (living part of wood) of the two tree species European beech (Fagus sylvatica) and Norway spruce (Picea abies). Along with the chemical composition of soil and saprolite calculated weathering indices such as the chemical depletion fraction (CDF) and the mass transfer coefficient (τ_(X_i)^X) are reported for regolith and bedrock. Further, the dataset contains phosphorus (P) concentrations measured by ICP-OES and UV spectrometry from various P fractions obtained by sequential extractions following the Hedley fractionation method. Additionally, the pH of soil and saprolite measured by a pH meter as well as the radiogenic Sr isotope ratio, namely 87Sr/86Sr measured by MC-ICP-MS for bulk bedrock and regolith are reported in the dataset. Finally, to estimate the landscapes lowering rate (total denudation) in situ 10Be concentrations were measured by accelerator mass spectrometry (AMS) on bedload sediment at the outlet of the catchment. The data presented here stem from sampling campaigns described in Uhlig et al. (2019) to which they are supplementary material to. Samples were mainly processed in the Helmholtz Laboratory for the Geochemistry of the Earth Surface (HELGES) and the GFZ section of Inorganic and Isotope Geochemistry (XRF analyses), the University of Bonn (P Hedley fractionation), and the University of Cologne - Centre for Accelerator Mass Spectrometry (AMS) (10Be measurements). This dataset represents the supplementary material to Uhlig et al. (2019). Tables (including data quality control) supplementary to the article are provided in pdf and xls formats. In addition, data measured in the course of the study is given in machine readable ASCII files. All samples are indexed with an International Geo Sample Number (IGSN). Sample metadata can be viewed by adding the IGSN to the “http://igsn.org/” URL (e.g. igsn.org/GFDUH00LT).