On October 23th 2000, the EU Water Framework Directive was finally adopted. The Directive was published in the Official Journal on December 22th 2000 and entered into force the same day. The Water Framework Directive expands the scope of water protection of all waters and sets clear objectives that a 'good status' must be achieved for all European waters by 2015 and that water use must be sustainable throughout Europe. According to the Directive, the individual member states are obligated to describe ecological objectives or goals for different waters. The aim of this project was to define ecological objectives for different biological quality elements for the Flemish transitional waters. In this document quality indices for benthos and phytoplankton have been presented. This document includes a study about the different approaches and methods used in Europe to define these ecological objectives. None of the existing indices was satisfactory and applicable on the Flemish transitional waters, neither for benthos nor for phytoplankton. This has to do with the complexity of transitional water systems. For the Flemish transitional waters no temporal or spatial reference is available. The reference is therefore based on the available knowledge about the ecological functioning of estuaries. Concerning phytoplankton, separate indices have been established for the salt and fresh water zones of an estuary. For brackish water, a natural mortality zone for plankton, indices would be pointless. The scoring system for phytoplankton takes into account the trophic status (including the important element silica), the photic status and the danger of flushing. This scoring system has a simple design and determination of the coefficients requires minimal effort. After evaluation by specialists and comparison with other scoring systems, we can state that the proposed phytoplankton index is promising. Nevertheless the index needs testing, because the available data of the Flemish transitional waters were used for its compilation. ...