In the context of an experimental approach to organic and inorganic mercury bio-accumulation by burrowing mayfly nymphs— Hexagenia rigida—, gills and different parts of the gut were investigated by light and electron microscopes. In the gut, two regions were studied: (1) mesenteron (midgut) characterized by cells with microvilli and a peritrophic membrane throughout this part, a lot of fungal hyphae being found on it; (2) proctodeum (hindgut) characterized by macrovilli, the apical face of cells being covered by a thick layer of chitin; many bacteria were observed at the bottom of macrovilli. The stomodeum (foregut) is extremely short. The gills are made up of six pairs of lamellae fringed with long filaments which are arranged on both sides of the long axis. Gills are constituted by tracheae and tracheoles, with a large canal for haemolymph circulation; muscle masses and nerve bundles were also observed. This structural approach shows that the nymph interface with the external environment, at gill and gut barrier levels, are quite different. Links between this structural and ultrastructural analysis and contamination mechanisms, via the trophic or direct route, are discussed; gills and gut could be transfer routes for mercury absorption, but also target organs for metal accumulation.