A short overview of fish-based assessment methods for aquatic systems is presented. Multimetric indices, as, e.g., the index of biotic integrity (IBI), firstly developed in USA and later adapted for European river basins and other countries, are shortly described. Non-multimetric indices are also discussed, e.g. the ichthyological index (II) and the index of ecological status of fish communities (ISECI), both proposed for monitoring Italian rivers. Moreover, statistical and predicting methods based on machine learning techniques are described. Finally, a new approach for developing standardised fish-based methods useful to assess ecological status of Italian rivers is proposed. Although rather complex, the use of bony fish in biomonitoring is promising and requires a multidisciplinary approach to be adopted.