The habitat heterogeneity hypothesis states that increased habitat heterogeneity promotes species diversity through increased availability of ecological niches. We aimed at describing the local-scale (i.e. nest and adjacent substrate) effects of nests of the sea lamprey ( Petromyzon marinus L.) as ecosystem engineer on macroinvertebrate assemblages. We hypothesized that increased streambed physical heterogeneity caused by sea lamprey spawning would modify invertebrate assemblages and specific biologic traits and promote reach-scale diversity. We sampled thirty lamprey nests of the Nive River, a river of the south western France with a length of 79.3 km and tributary of the Adour River, in three zones: the unmodified riverbed (upstream) and zones corresponding to the nest: the area excavated (pit) and the downstream accumulation of pebbles and cobbles (mound). The increased habitat heterogeneity created by lamprey was accompanied by biological heterogeneity with a reduced density of invertebrates (3777 ± 1332 individuals per m 2 in upstream, 2649 ± 1386 individuals per m 2 in pit and 3833 ± 1052 individuals per m 2 in mound) and number of taxa (23.5 ± 3.9 taxa for upstream, 18.6 ± 3.9 taxa in pit and 21.2 ± 4.5 taxa for mound) in the pit compared to other zones. However the overall taxa diversity in nest increased with 82 ± 14 taxa compared to the 69 ± 8 taxa estimated in upstream zone. Diversity indices were consistent with the previous results indicating a loss of α diversity in pit but a higher β diversity between a pit and a mound than between two upstream zones, especially considering Morisita index accounting for taxa abundance. Trait analysis showed high functional diversity within zones with a reduced proportion of collectors, scrapers, shredders, litter/mud preference and small invertebrates in mound, while the proportion of “slabs, blocks, stones and pebbles” preference and largest invertebrates increased. Pit presented the opposite trend, while upstream had globally intermediate trait proportions. Our results highlight important effects on species and functional diversity due to habitat heterogeneity created by a nest-building species, what can ultimately influence food webs and nutrient processes in river ecosystems.