Primary production dynamics are strongly associated with vertical density profiles, which dictate the depth of stratification and mixed layers. Climate change and artificial structures (e.g. windfarms) are likely to modify the strength of stratification and vertical distribution of nutrient fluxes, especially in shelf seas where fine scale processes are important drivers, affecting the vertical distribution of phytoplankton. To understand the effect of physical changes on primary production, identifying the linkage between density and phytoplankton profiles is essential. Here, the ecological relevance of eight density layers (DLs) obtained by multiple methods that define three different portions of the pycnocline (above, centre, below) was evaluated to identify a valuable proxy for subsurface Chlorophyll-a (Chl-a mg m-3) concentrations. The associations of subsurface Chl-a with surface and deep mixing were investigated by hypothesizing the occurrence at the same depth of any DL and the maximum Chl-a layer (DMC) using Spearman correlation, linear regression, and a Major Axis analysis. Out of 1237 observations of the water column exhibiting a pycnocline, 78 % reported DMCs above the bottom mixed layer depth (BMLD). This suggests that the BMLD is a boundary trapping Chl-a in shallow waters (≤ 120 m). BMLD constantly described Chl-a vertical distribution despite surface mixing indicators, suggesting a significant contribution of deep mixing processes in supporting subsurface production under specific conditions (e.g. prolonged stratification, tidal cycle, and bathymetry). Using BMLD for defining subsurface Chl-a could be a valuable tool for understanding the spatiotemporal variability of Chl-a in shelf seas, representing a potential variable for ecological assessments.