The effect of different urbanization levels on terrestrial biodiversity associated with riparian zones remains poorly studied, despite the important ecosystem services it provides in cities. Studies focused on aquatic ecosystems in urban streams reported decreases in ecological quality and species richness, and lack of sensitive taxa. Thus, we investigated the impact of urbanization on riparian zone flora and terrestrial invertebrates using as case studies nine urban streams spanning an urbanization gradient in the Portuguese city of Coimbra. An unexpectedly high number of taxa were identified (163 plants, 80 terrestrial invertebrates), 80% new registrations for the region and one endemic-rare plant. Yet, diversity varied across streams, β-diversity reaching 39% Bray-Curtis similarity and averaging 25%, due to many underrepresented terrestrial taxa (N = 62 observed only in one site). Variation across the urbanization gradient reached 59% in plants and 82% in terrestrial invertebrates. High numbers of non-native taxa (13%; N = 32), mostly plants, suggested urbanization factors, e.g. human interference and discharge variation, may have favored invasions. Indeed, constructed natural spaces along streams, like parks, supported less biodiversity. Moreover, plant richness, especially of riparian plants, was correlated negatively with percentages of surrounding impervious areas and positively with water quality. This shows urbanization has negative effects on riparian vegetation, and water quality impacts both aquatic and terrestrial communities. Our results stress urban streams as novel ecosystems constituted by high numbers of non-native taxa, and the significance of riparian zones for biodiversity preservation. Less intense intervention on riparian vegetation is recommended to increase biodiversity.