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Surface modified graphene oxide (GO) has received broad interest as a potential platform material for sensors, membranes, and sorbents, among other environmental applications. However, compared to parent (unmodified) GO, there is a dearth of information regarding the behavior of subsequently (secondary) modified GO, other than bulk natural organic matter (NOM) coating(s). Here, we systematically explore the critical role of organic functionalization with respect to GO stability in water. Specifically, we synthesized a matrix of GO-based materials considering a carefully chosen range of bound organic molecules (hydrophobic coatings: propylamine, tert-octylamine, and 1-adamantylamine; hydrophilic coatings: 3-amino-1-propanol and 3-amino-1-adamantanol), so that chemical structures and functional groups could be directly compared. GO (without organic functionalization) with varying oxidation extent(s) was also included for comparison. The material matrix was evaluated for aqueous stability by comparing critical coagulation concentration (CCC) as a function of varied ionic strength and type (NaCl, CaCl2, MgCl2, and MgSO4) at pH 7.0. Without surface derivatization (i.e., pristine GO), increased stability was observed with an increase in the GO oxidation state, which is supported by plate–plate Derjaguin, Landau, Verwey and Overbeek (DLVO) energy interaction analyses. For derivatized GO, we observed that hydrophilic additions (phi-GO) are relatively more stable than hydrophobic organic coated GO (pho-GO). We further explored this by altering a single OH group in the adamantane-x structure (3-amino-1-adamantanol vs. 1-adamantylamine). As expected, Ca2+ and monovalent co-ions play an important role in the aggregation of highly oxidized GO (HGO) and phi-GO, while the effects of divalent cations and co-ions were less significant for pho-GO. Taken together, this work provides new insight into the intricate dynamics of GO-based material stability in water as it relates to surface functionalization (surface energies) and ionic conditions including type of co- and counter-ion, valence, and concentration.