The seasonal variation in concentration of transparent exopolymer particles (TEP), particulate organic carbon (POC) and nitrogen (PON) were investigated together with floc size and the concentration of suspended particulate matter (SPM) along the cross-shore gradient, from the high turbid nearshore towards the low-turbid offshore waters in the southern Bight of the North Sea. The analyses of TEP, POC and PON result in a set of parameters that incorporate labile and refractory organic matter (OM) fractions. Our data demonstrate that biophysical flocculation cannot be explained by these heterogeneous parameters, but requires a distinction between a more reactive labile (“fresh”) and a less reactive refractory (“mineral-associated”) fraction. Based on all data we separated the labile and mineral-associated POC, PON and TEP using a semi-empirical model approach. The model’s estimates of fresh and mineral-associated OM show that great parts of the POC, PON and TEP are associated with suspended minerals, which are present in the water column throughout the year, whereas the occurrence of fresh TEP, POC and PON is restricted to spring and summer months. In spite of a constantly high abundance of total TEP throughout the entire year, it is its fresh fraction that promotes the formation of larger and faster sinking biomineral flocs, thereby contributing to reduce the SPM concentration in the water column over spring and summer. Our results show that the different components of the SPM, such as minerals, extracellular OM and living organisms, form an integrated dynamic system with direct interactions and feedback controls.