Urbanisation alters the natural hydromorphology of streams, affecting aquatic communities and ecological quality. Increasing efforts have been put into the rehabilitation of urban streams due to their importance for urban sustainability. Despite these efforts, many projects fail to achieve the improvement of aquatic communities. This study aims to provide specific recommendations to enhance the biological rehabilitation of urban streams by reviewing: (i) the impacts of urbanisation and climate change on urban stream hydrology, (ii) the responses of invertebrate assemblages to alterations in the hydrology and morphology of streams, and (iii) the hydromorphological rehabilitation measures applied to streams and their effect on invertebrate communities. This review found that commonly employed measures of habitat heterogeneity enhancement (such as the addition of meanders, boulders, and artificial riffles) are not enough to improve invertebrate communities. On the other hand, the most effective measures are those leading to the re-establishment of natural hydrological patterns and good water quality. Ultimately, an integrated ecohydrological approach that considers the entire watershed and its interactions between ecosystems and anthropological activities is the key to managing and rehabilitating urban streams.