Few-layered molybdenum disulfide (MoS2) nanosheets are poised to be at the core of low-voltage electronic device development. Upon environmental release, these two-dimensional (2D) structures can interact with abundant natural geocolloids. This study probes the role of dimensionality in modulating the aggregation behavior of 2D MoS2 nanosheets with plate-like geocolloids (i.e., homoionized kaolinite and montmorillonite clays). MoS2 nanosheets were exfoliated using an ethanol/water mixture, and aggregation kinetics were investigated with time-resolved dynamic light scattering at low monovalent salt concentrations and at three pH levels, in the presence and absence of Suwannee River humic acid (SRHA). Results indicate that pH and particle ratios are key to modulating the stability of MoS2/clay systems. At pH 4, aggregation of MoS2 increased with increasing MoS2/clay ratios and approached maximum values of 0.09 and 0.06 nm/s in the binary systems with montmorillonite and kaolinite, respectively. Electrostatic attraction facilitates heteroaggregation at pH values of 4 and 6; differences in the clay structures (i.e., face–face or face–edge aggregates) might explain the resulting MoS2/clay aggregate configurations, which were probed via the evolution of particle size distribution. The presence of only 0.1 mg/L SRHA drastically suppresses the heteroaggregation propensity of MoS2 nanosheets with geocolloids (to less than 0.01 nm/s at all pH values tested). The high stability of these heterogeneous systems under environmentally relevant conditions can increase the likelihood for cellular uptake and long-distance transport of MoS2.