Ice shelves around Antarctica can provide back stress for outlet glaciers and control ice sheet mass loss. They often contain narrow bands of thin ice termed ice shelf channels. Ice shelf channel morphology can be interpreted through surface depressions and exhibits junctions and deflections from flowlines. Using ice flow modeling and radar, we investigate ice shelf channels in the Roi Baudouin Ice Shelf. These are aligned obliquely to the prevailing easterly winds. In the shallow radar stratigraphy, syncline and anticline stacks occur beneath the upwind and downwind side, respectively. The structures are horizontally and vertically coherent, except near an ice shelf channel junction where patterns change structurally with depth. Deeper layers truncate near basal incisions. Using ice flow modeling, we show that the stratigraphy is ∼9 times more sensitive to atmospheric variability than to oceanic variability. This is due to the continual adjustment toward flotation. We propose that syncline-anticline pairs in the shallow stratigraphy are caused by preferential snow deposition on the windward side and wind erosion at the downwind side. This drives downwind deflection of ice shelf channels of several meters per year. The depth variable structures indicate formation of an ice shelf channel junction by basal melting. We conclude that many ice shelf channels are seeded at the grounding line. Their morphology farther seaward is shaped on different length scales by ice dynamics, the ocean, and the atmosphere. These processes act on finer (subkilometer) scales than are captured by most ice, atmosphere, and ocean models, yet the dynamics of ice shelf channels may have broader implications for ice shelf stability.