Ice shelves around Antarctica can restrict outlet glaciers and control ice-sheet mass loss. They often contain narrow, curvilinear tracts of thin ice termed ice-shelf channels. Their surface depressions display a morphology including deflections from flowlines and junctions. We investigate ice-shelf channels in the Roi Baudouin Ice Shelf using the radar data and ice-flow modeling. In the shallow radar stratigraphy near the ice-shelf front, syncline and anticline stacks occur beneath the northeastern (i.e. upwind) and the southwestern (i.e. downwind) flanks of the surface depression, respectively. These structures are horizontally coherent and occur over the entire ice column, except near an ice-shelf channel junction where patterns change structurally with depth. Truncation of layers near basal incisions occurs both near the grounding line and farther seawards. Using ice-flow modelling, we show that the stratigraphy is $\sim$9 times more sensitive to atmospheric than to oceanic perturbations, and interpret synclines and anticlines in the shallow stratigraphy with preferential snow deposition on the windward and wind erosion at the downwind side. This causes downwind deflection of ice-shelf channels of several meters per year. The depth variable structures show active modification of an ice-shelf channel junction by ocean melting or by differential flow. We conclude that many ice-shelf channels are seeded at the grounding line; however, their morphology farther seawards is shaped on different length scales by ice dynamics, the ocean, and the atmosphere. These processes act on sub-kilometer scales and outside the realm of most ice-, atmosphere- and ocean models yet they may have broader implications in terms of ice-shelf stability.