Clay minerals and cyanobacteria occur ubiquitously in nature, and both independently influence trace metal cycling due to their high specific surface areas and reactivity. Although the surface reactivity of each is well-studied, the reactivity of clay-cyanobacterial aggregates has received less attention. Here, we performed potentiometric acid-base titrations and Cd adsorption experiments on various concentrations of clay-cyanobacterial aggregates using three clay minerals (kaolinite, illite, and montmorillonite) and two model planktonic cyanobacteria, the freshwater species Synechocystis sp. PCC 6803 and marine species Synechococcus sp. PCC 7002. A component additivity surface complexation modeling (CA-SCM) approach was applied to study the impacts of the aggregation processes on the total surface reactivity. Results demonstrate that the CA-SCM approach effectively predicted the acid-base titration and Cd adsorption behaviors of aggregates at low aggregate concentrations (up to 2.5 g of clay/L for acid-base titration and 0.1 g of clay/L for Cd adsorption), indicating the additivity of the reactivity for the two components. However, at higher aggregate concentrations (25 g of clay/L for acid-base titration and 10 g of clay/L for Cd adsorption), the CA-SCM approach overestimates the acid-base titration and Cd adsorption behaviors for the aggregates, indicating significant surface site blockage during aggregation. Our SEM images show that both cyanobacterial species were covered by layered clay minerals at the surfaces and formed relatively larger aggregates at high aggregate concentrations than at low aggregate concentrations. Based on the combined results, we propose that the interaction between clays and cyanobacteria is relatively weak at low aggregate concentrations (e.g., <10 g of aggregate/L), but that significant obstruction of surface adsorption sites occurs at high aggregate concentrations (e.g., >10 g of aggregate/L), possibly due to the encrustation of bacteria by clay minerals. The implication of this work is that where turbid rivers discharge into estuaries or deltas with high primary phytoplankton productivity, aggregation (or flocculation) processes will cause the depression of surface reactivity of the aggregates and lead to a decrease in metal-binding capacity. Therefore, depending on whether the trace elements are nutrients (e.g., phosphorous) or potentially toxic (e.g., cadmium), this process has the potential to impact the marine biosphere. To ground truth this hypothesis, we further analyzed the correlation between total organic carbon (TOC) content and trace metal compositions in a compiled shale database and the results show clear negative correlation between Cd concentration and the concentration of TOC, Al and Si. Although this offers only an indirect assessment of the role of clay-plankton aggregation, as a first-order test it does indeed show that the aggregation between clay minerals and phytoplanktonic bacteria in estuaries is an essential factor that influences trace-elemental cycling.