During the next few years the Swedish Nuclear Fuel and Waste Management Co. (SKB) performs site investigations at two sites in Sweden for a future repository of spent nuclear fuel. Parallel an encapsulation plant is planned to encapsulate the spent fuel in copper canister according to the KBS-3 method. The purpose of the SR-Can safety assessment is to show the performance of the canister isolation at different sites for a repository at 500 meters depth in crystalline rock. Moreover SR-Can provides an example how the site specific safety assessment of a deep repository will be made in year 2006-2008. To able to calculate dose and risk for humans and the environment new assessment method were developed for the biosphere. These methods were based on a systems ecological modelling approach and used knowledge from landscape ecology to provide an integrated approach with hydrology and geology considering the discharges in a watershed and calculating consequences in terrestrial and aquatic ecosystems. A range of methods and tools were developed with the aid of GIS and the softwares Matlab/Simulink which facilitated the modelling and increased the understanding of the important processes in the landscape today and the next few thousands of years. In this paper an overview of the program and the novel methods are presented as well as some examples from performance calculations from a watershed in the Forsmark area considering effects on humans and ecosystems.