Background and Aims: In acidic soils, aluminum (Al) toxicity remains a critical crop limitation that can be ameliorated by organic amendments through Al complexation with high-molecular-weight carbon compounds, particularly fulvic and humic acids (FA and HA) However, no research discriminates between the direct effects of FA and HA on plant growth and the indirect effect that occurs through ameliorating Al toxicity. This study delineates the direct and indirect effects of FA and HA on plant growth. Methods: Eucalyptus and Hay FA and HA, and Al effects on maize (Zea mays) root growth were investigated using dilute nutrient solution. Five Al concentrations (0–270 µM) were combined with four organic acid (OA) treatments, including Nil-OA, FA40, and HA40 (each at 40 mg C L−1) and a combined treatment FA40HA40 (80 mg C L−1). Results: Eucalyptus FA and HA stimulated root growth by ~20% compared with root growth in the Nil-OA (17.4 cm). In the absence of Al, Hay FA and HA inhibited root growth (by ~20%) compared with the Nil-OA but the addition of Al resulted in stimulation of root growth. In the presence of FA and HA, root growth was not inhibited by nominally toxic monomeric Al (Al3+) concentrations (~20 µM Al). However, when expressed on a relative basis to remove the direct effect of the ligand, the response was consistent with Al toxicity. Conclusions: The effects of FA and HA were either inhibitory or stimulatory depending on the source while both sources of FA and HA mitigated Al toxicity through complexation. The study provides mechanistic data that highlights limitations of soil bioassays where the direct effects of organic ligands on root growth are confounded with the indirect effect of their reduction of Al toxicity. These two independent processes must be considered in evaluating the amelioration of Al by organic amendments.