Beaver populations are increasing throughout Europe and especially in Switzerland. Beaver are major ecological engineers of fluvial systems, dramatically influencing river morphology, ecohydrology and, consequently, aquatic and terrestrial biota. This study compared macroinvertebrate assemblages and trophic structure at two beaver complexes with contrasting topography in Switzerland over an annual cycle. One complex (Marthalen) was in a low gradient open basin, whereas the other complex (Flaach) flowed through a higher gradient ravine-like basin. Both complexes were embedded in an overall agricultural landscape matrix. Water physico-chemistry differed between the two complexes with nitrogen, phosphorus, and DOC being higher at Marthalen than at Flaach. Both complexes showed strong seasonality in physico-chemistry, but retention of nutrients (N, P) was highest in summer and only at Marthalen. Both complexes also showed strong seasonality in macroinvertebrate assemblages, although assemblages differed substantially between complexes. At Marthalen, macroinvertebrate assemblages were predominantly lentic in character at 'pool' sites within the complex. At Flaach, lotic macroinvertebrate assemblages were common at most sites with some lentic taxa also being present. Dietary shifts based on carbon/nitrogen stable isotopes occurred in spring and summer among sites at both complexes (autochthonous resource use increasing over allochthonous resource use downstream), although being most pronounced at Marthalen. In contrast, similar resource use across sites occurred in winter within both complexes. Although beaver significantly influenced fluvial dynamics and macroinvertebrate assemblage structure at both complexes, this influence was most pronounced at Marthalen where beaver caused the system to become more wetland in character, e.g., via higher hydraulic residence time, than at Flaach. We conclude that topography can shape beaver effects on fluvial systems and resident biota.