The understanding about the development of benthic invertebrate communities as a function of abiotic influencing factors in aquatic ecosystems is of essential scientific relevance for the assessment of the ecological status of rivers and streams. For the development of interdependencies between benthic invertebrates, hydromorphology and saprobity, 409 species lists of the macroinvertebrates were provided. They were aggregated with morphological features and analysed with different uni- and multivariate statistical methods. On the basis of the used analyses, the following results were achieved: (a) seven ecological relevant morphological features with significant influence to benthic invertebrate community could be identified, (b) on the basis of the present database, the structural and functional composition of the benthic invertebrates can not be differ river type specific (type 5 and 5.1) and (c) if the saprobic pressure decrease, the organic pressure superpose the hydromorphology. The values of the biological attributes are low in spite of near natural morphological conditions. For an ecological efficiency stream habitat assessment, the identified relevant morphological parameters have to consider. The “morphological characteristic curves” are well describing the results of a local monitoring. This application-oriented instrument can be used for (a) the operationalisation of environmental objectives, (b) the development and adaption of monitoring strategies and (c) the derivation and prioritisation of ecological and economic efficiency measurements for an integrated river management.