The automated processing of environmental monitoring data is documented on ARROW (Assessment and Reference Reports of Water monitoring) project. It is the project of implementation of EU Water Framework Directive in the monitoring of surface waters of the Czech Republic and covers all aspects of this problem from data sampling to informatics solution (focusing on the ecological state). The project is based on long term development of this field in the Czech Republic and it is carried out under the supervision of the Ministry of the Environment of the Czech Republic. The important part of the ARROW project is the development and implementation of a Czech approach to the evaluation of the ecological state of surface waters using an analysis of monitoring data. The main idea of the system is an approach based on a network of reference sites, multimetric indices and robust multivariate modelling of expected environmental and biological conditions. The approach presented is compatible with the EU Water Framework Directive and implemented in the national-wide information system of the ecological state of surface waters of the Czech Republic.