The method based on original metric called Hydromorphological Index for Rivers (HIR) was developed in 2017 for the purpose of the monitoring of the hydromorphological status of flowing waters in Poland. It fulfils requirements of the EU Water Framework Directive (WFD). It allows assessment of both lowland rivers as well as mid-altitude and highland streams. The proposed system can be used to assess the natural and heavily modified rivers as well as artificial channels. The basis of the proposed system is a field survey, which is supplemented by analysis of Geographic Information Systems (GIS) data and remote sensing materials. Analysis of the GIS data and remote sensing materials already enable to estimate preliminary classification of hydromorphological status of non-surveyed water bodies. Basing on the field survey, the principal HIR value can be estimated for the considered river site and comparing with the reference conditions the hydromorphological quality status in the five-class system can be calculated. Properly selected, representative survey sites (one or more depending on the heterogeneity of the environment), enable classification and evaluation of entire surface water bodies in the framework of the national environmental monitoring. The GIS component of the HIR proved to be useful in verifying the determination of heavily modified water bodies and in assessing the needs of river restoration. I was also applied in development of the National river restoration program, for predicting the impact of proposed restoration measure on the state of hydromorphology.