This work focuses on the North Aegean Sea deep chlorophyll maximum (DCM) dynamics, as revealed during the first glider mission over the continental shelf and slope of the Thracian Sea and along the Athos basin, and presents a conceptual model on the response of the DCM in relation to the prevailing stratification/mixing of the water column. Water temperature, conductivity, salinity, chlorophyll-a, CDOM, DO and particle backscatter data (bb700), were recorded during this underwater glider mission in summer 2019. Daily satellite data from Sentinel 3 complemented the glider collected data to validate the satellite-derived estimates of surface Chlorophyll-a levels. The high-resolution physical and chemical observations were analyzed emphasizing on thermal stratification, pycnocline strength, CDOM and dissolved oxygen vertical distribution and the presence of deep chlorophyll maximum (DCM). DCM statistical characteristics were derived by fitting a Gaussian model on the chlorophyll-a profiles. The mean DCM was observed at 76 ± 14.5 m depth, located below the euphotic layer, estimated at 64 ± 2.1 m, with the water column dynamics affecting directly its depth, thickness and peak prominence. The satellite-derived chlorophyll-a, integrated within the euphotic layer, was found in fair agreement to the integrated chlorophyll-a values from surface to optical depth recorded by the glider. Chl-a at the DCM were found up to 0.60 mg m−3, the vertically-integrated pigment content was estimated at 45 ± 14 mg m−2 and the values of Optical Community Index (OCI) illustrate the dominance of small-sized plankton. The increased variability in the particulate backscattering coefficient bb700 in Thracian Sea shelf and slope deep waters seems related to sediment resuspension. CDOM levels increased from 0.76 ppb at the sea surface to 1.11 ppb at 40 m depth, being positively correlated to Chl-a within the DCM. CDOM concentration increased steadily at intermediate and deeper waters up to 1.34 ± 0.07 ppb. DO profiles revealed the presence of an oxycline in the DCM layer, capable to oxygenate the intermediate and deeper waters (+3 × 10−3 ml/L/m). Bottom DO in Athos basin was measured at 5.0 ml L−1, indicating that the apparent oxygen utilization in Athos Basin is approximately 50 μmol L−1.