In this work we report short-term measurements of the thermohaline structure and velocity field inside a narrow submarine canyon by means of a yo-yo–like profiler. An Aqualog profiler was deployed inside the Besòs Canyon in the northwestern Mediterranean continental margin, providing a unique data set on the vertical evolution of water column characteristics with unprecedented fine-scale spatial and temporal resolution. The observations reported here show a very dynamic transient short-term response with a complex vertical structure not observed previously in any submarine canyon of this region. The vertical distribution of water masses was characteristic of the western Mediterranean basin with Atlantic waters (AW) at the surface, Western Intermediate waters (WIW) in the middle and Levantine Intermediate (LIW) waters below. Turner angle and empirical orthogonal functions show that double-diffusive and isopycnal mixing are the main dominant processes at small scales. The interfaces of the three layers exhibit highly vertical excursions in relatively short times. At the surface, deepening of AW was observed, associated with flow intensification events. Deeper in the water column, within the submarine canyon confinement, the WIW-LIW interface uplifts about 100-150 m. These motions are associated with relatively up- and down-canyon–enhanced current events (up to 15-20 cm s–1 at 500 and 800 m depths) along the canyon axis. The time scales of the vertical variability were concentrated in a broad band around the semi-diurnal and local inertial frequencies within the WIW and LIW layers.