In integrated river basin management, measures for reaching the environmental objectives can be evaluated at different scales, and according to multiple criteria of different nature (e.g. ecological, economic, social). Decision makers, including responsible authorities and stakeholders, follow different interests regarding criteria and scales. With a bottom up approach, the multi criteria assessment could produce a different outcome than with a top down approach. The first assigns more power to the local community, which is a common principle of IWRM. On the other hand, the development of an overall catchment strategy could potentially make use of synergetic effects of the measures, which fulfils the cost efficiency requirement at the basin scale but compromises local interests. Within a joint research project for the 5500 km2 Werra river basin in central Germany, measures have been planned to reach environmental objectives of the European Water Framework directive (WFD) regarding ecological continuity and nutrient loads. The main criteria for the evaluation of the measures were costs of implementation, reduction of nutrients, ecological benefit and social acceptance. The multi-criteria evaluation of the catchment strategies showed compensation between positive and negative performance of criteria within the catchment, which in the end reduced the discriminative power of the different strategies. Furthermore, benefit criteria are partially computed for the whole basin only. Both ecological continuity and nutrient load show upstream-downstream effects in opposite direction. The principles of "polluter pays" and "overall cost efficiency" can be followed for the reduction of nutrient losses when financial compensations between upstream and downstream users are made, similar to concepts of emission trading.