© Inter-Research 2016. Understanding the processes driving the distribution of mid-water prey such as euphausiids and lanternfish is important for effective management and conservation. In the vicinity of abrupt topographic features such as banks, seamounts and shelf-breaks, mid-water faunal biomass is often elevated, making these sites candidates for special protection. We investigated the spatial distribution of water column acoustic backscatter - a proxy for macrozoo - plankton and fish biomass - in the 9 km transition zone between the pelagos and coral atolls in the Chagos Archipelago (6° N, 72° E). The purpose was to determine the magnitude and distance over which bathymetry may enhance biomass in the mid-water, and thereby identify the scale over which static topographic features could influence the open ocean. Two distinct sound scattering layers were identified, from the surface to 180 m and from 300 to 600 m, during daytime. Both layers exhibited significant increases in backscatter near features. Close to features, the shallow layer backscatter was ca. 100 times higher and was driven partly by increasing numbers of larger individuals, evident as single target echoes. We determine the regional scale of influence of features on pelagic biomass enhancement to be ca. 1.8 km in the Chagos Archipelago, and suggest possible ecological explanations that may support it. Our approach determining the scale of influence of bathymetry should be applied during the process of marine reserve design, in order to improve protection of mid-water fauna associated with topographical features, such as seamounts and coral reefs.