Marine organisms are frequently exposed to pollutants, including trace metals, derived from natural and anthropogenic activities. In order to prevent environmental pollution, different approaches have been applied to remove pollutants from waste water and avoid their discharge into aquatic systems. However, organisms in their natural aquatic environments are also exposed to physico-chemical changes derived from climate change-related factors, including temperature increase. According to recent studies, warming has a negative impact on marine wildlife, with known effects on organisms physiological and biochemical performance. Recently, a material based on graphene oxide (GO) functionalized with polyethyleneimine (PEI) proved to be effective in the remediation of mercury (Hg) contaminated water. Nevertheless, no information is available on the toxic impacts of such remediated water towards aquatic systems, neither under actual nor predicted temperature conditions. For this, the present study assessed the toxicity of seawater, previously contaminated with Hg and remediated by GO-PEI, using the clam species Ruditapes philippinarum exposed to actual and a predicted temperature conditions. The results obtained demonstrated that seawater contaminated with Hg and/or Hg+GO-PEI induced higher toxicity in clams exposed to 17 and 22 °C compared to organisms exposed to remediated seawater at the same temperatures. Moreover, similar histological and biochemical results were observed between organisms exposed to control and remediated seawater, independently of the temperatures (17 and 21 °C), highlighting the potential use of GO-PEI to remediate Hg from seawater without significant toxicity issues to the selected marine species.