Active margins host more than half of submarine canyons worldwide. Understanding the coupling between active tectonics and canyon processes is required to improve modeling of canyon evolution and derive tectonic information from canyon morphology. In this paper we analyze high-resolution geophysical data and imagery from the Cook Strait canyon system (CS), offshore New Zealand, to characterize the influence of active tectonics on the morphology, processes, and evolution of submarine canyons, and to deduce tectonic activity from canyon morphology. Canyon location and morphology bear the clearest evidence of tectonic activity, with major faults and structural ridges giving rise to sinuosity, steep and linear longitudinal profiles, cross-sectional asymmetry, and breaks in slope gradient, relief, and slope-area plots. Faults are also associated with stronger and more frequent sedimentary flows, steep canyon walls that promote gully erosion, and seismicity that is considered the most likely trigger of failure of canyon walls. Tectonic activity gives rise to two types of knickpoints in the CS. Gentle, rounded and diffusive knickpoints form due to short-wavelength folds or fault breakouts. The more widespread steep and angular knickpoints have migrated through canyon-floor slope failures and localized quarrying and/or plucking. Migration is driven by base-level lowering due to regional margin uplift and deepening of the lower Cook Strait Canyon, and is likely faster in larger canyons because of higher sedimentary flow throughput. The knickpoints, nonadherence to Playfair’s Law, linear longitudinal profiles, and lack of canyon-wide, inverse power law slope-area relationships indicate that the CS is in a transient state, adjusting to perturbations associated with tectonic displacements and changes in base level and sediment fluxes. We conclude by inferring unmapped faults and regions of more pronounced uplift, and proposing a generalized model for canyon geomorphic evolution in tectonically active margins.