Aquatic macrophytes are an integral component of freshwater ecosystems, acting as primary producers, providing habitat for other aquatic organisms, and driving nutrient cycling. On the other hand, trace element pollution caused mainly by human activities such as mining and industrial runoff or agricultural practices threatens their health and performance. This chapter will explore the impacts of heavy metal pollutants such as mercury (Hg), lead (Pb), and cadmium (Cd), in addition to other trace elements, on macrophytes. We have discussed here that aquatic macrophytes respond at the physiological, biochemical, and ecological levels to trace element contamination. These include changes to growth, morphology, photosynthesis, nutrient uptake, and reproductive processes. Furthermore, the effect of trace element contamination on food web dynamics, trophic interactions, and ecosystem-level outcomes has been discussed in depth, emphasizing the overall impacts on biodiversity, habitat quality, and overall ecosystem resilience. This chapter adds to our understanding of the intricate interactions between aquatic macrophytes and trace element pollutants by reviewing recent research findings and filling in knowledge gaps. It further underscores the crucial need for integrated conservation and management strategies to help maintain the integrity of freshwater ecosystems.