The increasing contamination of aquatic ecosystems by heavy metals, persistent organic pollutants (POPs), endocrine-disruptor chemicals (EDCs), and microplastics presents a significant challenge for biodiversity conservation and environmental management. In light of these challenges, aquatic reptiles, such as turtles and crocodilians, are valuable model organisms for biomonitoring due to their unique physiology, bioaccumulation abilities, and site fidelity. This chapter highlights the biological and ecological traits that make these animals effective for detecting pollutants and analyzing their chronic impacts. Aquatic reptiles are particularly vulnerable to biomagnification, as they accumulate toxins like mercury, lead, and organochlorine pesticides in their tissues, offering insights into environmental health. Noninvasive sampling methods enable ongoing monitoring without harming individuals, which is crucial for threatened species. Integrating aquatic reptiles into biomonitoring programs is essential for guiding public policies, mitigating pollution, and protecting aquatic ecosystems and biodiversity. This chapter advocates for a broader application of aquatic reptiles in biomonitoring programs to address the intertwined challenges of chemical contamination and global climate change.