Anal papillae of caddisflies are peripheral organs responsible for osmoregulation and detoxification. Investigation of morphological abnormalities in the anal papillae of Hydropsyche angustipennis enriched with using SEM-EDX analysis (scanning electron microscopy-energy dispersive X-ray analysis), was used to assess heavy metal pollution levels in urban streams receiving surface runoff. Heavy metal ions not previously detected in water and tissue samples were detected using SEM-EDX method. Morphological irregularities were most frequently observed in larvae from the most contaminated streams. Heavy metals were almost 10 times more concentrated in darkened papillae than in pale, normal-shaped papillae. The present study confirms that SEM-EDX microscopy is an effective method as a support of standard heavy metal bioassays, especially if there is a necessity to detect trace elements in very low concentrations or incidental appearance of some ions in the water.