Anthraquinone-based molecules are promising electroactive materials for use in aqueous organic flow batteries. At high concentrations in aqueous solutions, the well-known negolyte molecule anthraquinone disulfonic acid (AQDS) molecule has been observed to aggregate under near-neutral and acidic conditions. Aggregation has been hypothesized to be directly linked to observed concurrent capacity reduction. In this study, we investigated three different water-soluble anthraquinones in electrolytes of varying compositions and pH to gain further insight into the possible causes of capacity loss. We used low-field benchtop 1H-NMR and diffusion NMR measurements directly in non-deuterated aqueous flow-battery electrolytes to investigate molecular aggregation. Single-cell testing was performed under exhaustive electrolysis conditions to determine the number of electrons exchanged per molecule. We observed a decrease in the number of electrons exchanged per molecule in the presence of carbonate ions due to CO2 adduct formation. The aggregation constants were determined from both concentration-dependent chemical shifts and self-diffusion coefficients. We show that aggregation of the oxidized form of all three molecules studied here occurs under near-neutral and alkaline conditions and does not affect the number of accessible e−.