In aquaponic farming, there is a potential risk that heavy metals will contaminate the water, which can lead to heavy metal accumulation in the plants. Our research investigated the accumulation of mercury (Hg) and lead (Pb) under aquaponic conditions and the effect of their increased presence on the uptake of other macro- and micronutrients using watercress (Nasturtium officinale) as a model plant. The potential modifying effect of humic acid on heavy metal accumulation was also investigated. Adding Hg and Pb increased the mercury and lead levels of the watercress plants to over 300 µg kg-1, while the addition of humic acid significantly reduced the concentration of both mercury and lead in the plants compared to plants treated with heavy metals alone, from 310.647 µg kg-1 to 196.320 µg kg-1 for Hg and from 313.962 µg kg-1 to 203.508 µg kg-1 for Pb. For Fe and Mn, higher values were obtained for the Hg + humic acid treatments (188.13 mg kg-1 and 6423.92 µg kg-1, respectively) and for the Pb + humic acid treatments (198.26 mg kg-1 and 6454.31 µg kg-1, respectively). Conversely, the Na, K, Cu levels were lower compared to those in plants treated with heavy metals alone. Our results demonstrated that watercress can accumulate mercury, leading to high levels, even above food safety standards, highlighting the importance of water quality control in aquaponic systems. Furthermore, these results suggest that watercress could be used as a natural filter in recirculation systems. The addition of humic acid significantly reduced the accumulation of heavy metals and altered the element content in the plant.