We compared biomass and community structure of macroinvertebrates among 3 flow zones (deep, rapid, flat) of riffles at 3 sites in a gravel-bed river. We evaluated bed stability in these zones with a 2-dimensional hydrodynamic simulation over a range of discharge levels. Deep zones had higher flow velocity and coarser bed materials than other zones. Rapid zones were shallower with higher flow velocity than flat zones. The probability of bed movement was greatest in rapid zones and was lowest in deep zones based on bed shear stress and the size of bed materials. Total macroinvertebrate biomass was dominated by filterer insects and was highest in deep zones and lowest in rapid zones across the sites. This trend was most conspicuous for taxa that build retreats on stones, such as net-spinning caddisflies, which have a sessile life form and prefer stable environments. The trend was less apparent for taxa that move freely on the bed, such as baetid and heptageniid mayflies. The macroinvertebrate community differed between the middle and peripheral areas at deep zones. Peripheral areas were dominated more by taxa that stay under stones. The channel bed topography in deep zones of riffles is likely to support high macroinvertebrate biomass by providing greater bed stability and higher water flow, the combination of which is relatively uncommon in gravel-bed rivers.