The deep-water region offshore NW Borneo is an active fold-and-thrust belt that hosts a significant number of proven hydrocarbon accumulations. In the past, two mechanisms have been discussed as primary control for Neogene to Holocene folding and thrusting in this deep-water province: (1) basement-driven crustal shortening and (2) gravity-related delta tectonics. In this study, new, balanced interpretations of regional, crustal-scale, depth-migrated, two-dimensional (2-D), multichannel seismic-reflection profiles are presented that provide for the first time quantitative data on tectonic shortening throughout the entire deep-water fold-and-thrust belt of NW Borneo. We use our tectonic restorations to compare the amount of deep-water shortening on the NW Borneo slope to the amount of extension across the NW Borneo shelf. A key result of this balancing study is the observation that Pliocene to Holocene gravity-driven shortening decreases from south to north, while the total amount of shortening increases slightly to the north. Consequently, the amount of purely basement-driven compression along NW Borneo is strongly inferred to increase toward the north. Because most of the shortening is late Pliocene and younger, we interpret the tectonic shortening to be ongoing.