Fate and transport of the engineered nanomaterials (ENMs) in aquatic systems has been increasingly concerned due to their potential human exposure and reported toxicity to the living organisms. The ubiquitous naturally occurring colloids (NOC) is an important impacting factor controlling the aqueous stability and subsurface transport of ENMs in porous media. This study investigated the effect of kaolinite on the aggregation, stability and subsurface mobility of carboxyl-functionalized multi-walled carbon nanotubes (COOH-MWCNT) under a range of environmentally relevant solution conditions. The increase of ionic strength and decrease of pH enhanced the heteroaggregation. CNT and kaolinite can form both primary and secondary heteroaggregates under different solution conditions. The effect of heteroaggregation strongly depends on the CNT-to-kaolinite ratio; it can either increase or decrease the stability of the suspension depending on the structure of the heteroaggregates formed. Ca2+ and dissolved NOM played opposite roles on the stability of CNT. The addition of Ca2+ induced the heteroaggregation through bridging effect and charge screening while NOM hindered the aggregation via steric effect in low Ca2+ conditions. When Ca2+ reached a high concentration range, the effect of Ca2+ dominated and induced large heteroaggregates, destabilizing the CNT-kaolinite system. In natural surface waters, CNT exhibits decreased stability, a notable portion of which is attributed to the naturally occurring colloids. The effect of other water quality parameters (e.g., ionic composition) also contributes to the decreased stability. Flow cytometry, a common technique for cell analysis in biological field, was applied in analyzing aggregations in Alexa Fluor 633 dyed carbon nanotubes (AFCNT) and kaolinite mixture under various pH and ionic strength conditions. By testing the extremely low concentrations of AFCNT and kaolinite mixture samples, the flow cytometer rapidly provided data needed in quantitatively determining the degree of homo- and heteroaggregations. It can be applied on future aggregation studies of ENM-NOC systems and provide meaningful information for the risk management of ENMs in aquatic environments. The mobility of CNT in porous media is strongly dependent on the degree of CNT-kaolinite heteroaggregation and the formation of the aggregates. Results demonstrated that significant CNT-kaolinite heteroaggregations occurred under extremely low pH (pH=3 in 1 mM NaCl) or extremely high ionic strength (pH=9, 100 mM NaCl) conditions. Under the conditions when large secondary aggregation formed at low pH, kaolinite hindered CNT mobility through straining effect. However, CNT transport was facilitated by kaolinite when primary heteroaggregates are the main formation in high ionic strength and high pH. When there were no CNT-kaolinite interactions, CNT mobility was enhanced probably because kaolinite competed with CNT for the adsorption sites on porous media. Findings in the study highlighted the important role of naturally occurring colloids, dissolved natural organic matter and solution chemistry on the environmental fate and transport of CNT. It provides fundamental information for the risk assessment of CNT in natural water systems.