How can we estimate the negative externalities of agriculture at the national level, and attribute these to specific production activities and outputs? The paper presents a method that calculates the mass flow in the whole agricultural sector including inputs from other sectors, and that allows to analyse resource use and emissions, e.g. of greenhouse gases. Data inputs are the German economic accounts for agriculture, farm structural survey and market statistics, as well as environmental statistics. In the framework of the German agricultural sector model RAUMIS, material flows within the agricultural sector are described, as well as inputs from other German sectors and imports. Through a processanalytical approach, all information is integrated and matrices of resource use and emissions for all agricultural production activities are generated. A monetary allocation is used to identify the respective activities that are responsible for emissions, including indirect emissions in upstream sectors. Related to the market output, cumulative emissions per unit of output can be computed. Results for the period from 1995 to 2007 show the trend of resource uses and emissions for the national average values of important commodities such as milk and meat.