Benthic macroinvertebrates are widely used as indicators of the health of freshwater ecosystems, responding both to water quality and to the hydromorphological integrity. In urban streams, evaluations can be tricky for the synergistic effects of multiple stressors and confounding factors. In these situations, the most broadly used multimetric indices can be used to assess the overall damage to the invertebrate community and, thus, the overall anthropogenic pressure, but they do not allow to understand the specific causal effects. Particularly, habitat loss due to morphological alterations can be difficult to evaluate, especially due to the often concurrent disturbance caused by water pollution. We used a multivariate approach to focus on the characteristics of the streams and rivers in an urban district and to define which macroinvertebrate metrics should be used to assess the influence of the different kinds of alteration in a severely damaged environment. Some metrics enabling the assessment of habitat loss (ratio of oligochaeta, ratio of filterers) were identified. These metrics may help to raise a better awareness in the evaluation of river restoration success and, thus, in the support of decision-making processes.