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Several Alpine streams are currently changing from perennial to intermittent systems with expected detrimental consequences on benthic invertebrates, through the alteration of hydrological conditions, substrate composition, and trophic resources. We examined the ecological niche of three phylogenetically-related scraper macroinvertebrates, namely Ecdyonurus, Epeorus, and Rhithrogena (Ephemeroptera, Heptageniidae) experiencing recurrent summer dewatering events in perennial and intermittent stretches in 13 Alpine streams. We evaluated the overlap among the ecological niches of the three examined taxa in terms of hydraulic stress, substrate coarseness, and total primary production and we investigated their ecological preferences in perennial and intermittent sites. Our results showed a broad overlap of their ecological niches, suggesting exploitative competition among the examined taxa. Their ecological niches were smaller in intermittent than perennial sites, pointing out a reduction of available microhabitats. All groups were favored by substrate coarseness and total primary production in reach types, while the hydraulic stress showed an opposite effect in perennial (negative) and intermittent (positive) sites. Overall, our results emphasize how stream physical parameters play a key role in determining the ecological niche of Heptageniidae and underline how benthic communities in intermittent sections of previously perennial Alpine streams are currently under pressure.