The assessment of running water quality has a long tradition in the Czech Republic, but in the past it focused on the evaluation of organic pollution using the saprobic system. Considering the modern trends of stream ecological status evaluation in water management a new assessment system named PERLA was developed. The system is a complex of biological methods of ecological status assessment of running waters and connected activities in the Czech Republic. It involves 300 reference sites with respective biotic and abiotic data and a prediction model using a newly developed software HOBENT. The model generally follows the published mathematical principles of RIVPACS and represents the site specific and stressor non-specific approaches. The HOBENT software allows the prediction of the target assemblage of benthic macroinvertebrates for any site based on a set of environmental variables (latitude, longitude, distance from source, altitude, slope, catchment area, and stream order) which characterise the site. The predicted assemblage can be compared with the fauna observed at the same site. The comparison makes it possible to evaluate the extent of disturbance, expressed by index B. The model allows to evaluate spring, summer, and autumn seasonal data of the majority of wadable streams in the Czech Republic. The practical application of the PERLA system has started in 2001.