Given the poor status of the European eel (Anguilla anguilla) population, good assessments are essential to optimise recovery measures. Quantifying eel stock size is challenging given the fractal nature of the distribution of eels, particularly in The Netherlands with its dense interconnected network of drainage ditches, rivers and lakes. Dynamic demographic models as used by others are inappropriate in this delta with a demand for regional information on stock size. We therefore estimated the standing eel stock biomass for all freshwater water bodies, using fish monitoring data collected under the Water Framework Directive and a static GIS approach. Density data were extrapolated to total biomass estimates using GIS data concerning water type, surface area and bank length, and biological parameters obtained from biological data. The analysis yielded density and biomass estimates of the total eel and silver eel stock, with most silver eel biomass being confined to a few coastal regions. The main conclusion is that over half of the Dutch eel biomass is found in the small, regionally managed waters, revealing a crude underestimation of the eel biomass in the 2009 Dutch Eel Management Plan. The silver eel biomass estimate presented here is two to three times higher than previous estimates. Providing spatial information on eel biomass will aid in prioritising management measures to reduce anthropogenic mortality.