<p>Urbanisation adversely affects aquatic organisms by changing environmental conditions and decreasing biodiversity, which favours pollution-tolerant species. The objectives were to define the spatio-temporal patterns of the Chironomidae species assemblage and characterise the aquatic habitats in relation to the dominant taxa and their physicochemical characteristics, and to determine the possible Chironomidae species assemblages as indicators of water quality using Chironomidae Pupal Exuviae Technique. Over a 2-year period, we collected pupal exuviae from urban and control streams, by analysing species attributes and corresponding habitat conditions. The findings revealed that urbanisation significantly reduced species richness and diversity in urban streams compared to reference sites. Pollution indicator species were identified, indicating that Chironomidae composition can be a reliable measure of water quality and environmental impacts in aquatic ecosystems. Urban streams showed elevated nutrient levels (P-PO₄ &gt; 2&#xa0;mg P.l⁻¹; N-NO₃ &gt; 0.5&#xa0;mg N.l⁻¹; N-NH₄ &gt; 1.5&#xa0;mg N.l⁻¹; DBO5 &gt; 20&#xa0;mg O₂.l⁻¹; DQO &gt; 60&#xa0;mg O₂.l⁻¹) and decreased vegetation cover (&lt; 20%), negatively affecting diversity and favouring pollution-tolerant species like <i>Chironomus calligraphus</i> and <i>Cricotopus</i> sp.1. The findings underscore the importance of species-level identification for effective biomonitoring, with the Chironomidae Pupal Exuviae Technique demonstrating strong efficacy in assessing water quality. Future research should focus on refining species-level identification and advancing Chironomidae-based bioindicator approaches to better evaluate the health of urban aquatic ecosystems.</p>