Natural wetlands are ecosystems with multiple biotic and abiotic components in constant interaction, covering 6% of the planet’s surface. These ecosystems are crucial in preserving biodiversity, regulating the water cycle, and preventing soil erosion. However, high levels of anthropogenic pollution are reported in natural wetlands, especially due to the presence of emerging pollutants. Therefore, the objective of the present work is to review the presence and behavior of emerging contaminants in natural wetlands, as well as the strategies implemented for their restoration. The presence of pesticides such as pentachlorobenzene (62 ng g−1) and orisastrobin (700 ng L−1), drugs such as tramadol (222 ng L−1) and paracetamol (168 ng L−1), and personal care products such as triclosan in concentrations in the order of 72 ng μL−1 have been reported in these environmental matrices. To mitigate this problem, significant progress has been made in restoration and treatment, showing improvements in water quality and habitat recovery. For example, technologies such as phytoremediation and the use of activated carbon in adsorption processes have made it possible to eliminate hydrophobic organic compounds. In addition, microbial restoration and hydrology management prevent and reduce pollution levels significantly. Finally, it is crucial to implement integrated measures that include source reduction, active habitat restoration, and riparian zone protection to mitigate adverse effects and ensure the sustainability of natural wetlands.