Submesoscale processes have a determinant role in the dynamics of oceans by transporting momentum, heat, mass, and particles. Furthermore, they can define niches where different phytoplankton species flourish and accumulate not only by nutrient provisioning but also by modifying the water column structure or active gathering through advection. In coastal areas, however, submesoscale oceanic processes act together with coastal ones, and their effect on phytoplankton distribution is not straightforward. The present study brings the relevance of hydrodynamic variables, such as vorticity, into consideration in the study of phytoplankton distribution, via the analysis of in situ and remote multidisciplinary data. In situ data were obtained during the ETOILE oceanographic cruise, which surveyed the Capbreton Canyon area in the southeastern part of the Bay of Biscay in early August 2017. The main objective of this cruise was to describe the link between the occurrence and distribution of phytoplankton spectral groups and mesoscale to submesoscale ocean processes. In situ discrete hydrographic measurements and multi-spectral chlorophyll a (chl a) fluorescence profiles were obtained in selected stations, while temperature, conductivity, and in vivo chl a fluorescence were also continuously recorded at the surface. On top of these data, remote sensing data available for this area, such as high-frequency radar and satellite data, were also processed and analysed. From the joint analysis of these observations, we discuss the relative importance and effects of several environmental factors on phytoplankton spectral group distribution above and below the pycnocline and at the deep chlorophyll maximum (DCM) by performing a set of generalized additive models (GAMs). Overall, salinity is the most important parameter modulating not only total chl a but also the contribution of the two dominant spectral groups of phytoplankton, brown and green algae groups. However, at the DCM, among the measured variables, vorticity is the main modulating environmental factor for phytoplankton distribution and explains 19.30 % of the variance. Since the observed distribution of chl a within the DCM cannot be statistically explained without the vorticity, this research sheds light on the impact of the dynamic variables in the distribution of spectral groups at high spatial resolution.