Graphene-based materials, including graphene oxide (GO) and functionalized derivatives, have demonstrated exceptional potential in addressing environmental challenges related to heavy metal detection and wastewater treatment. This review presents the latest advancements in graphene-based electrochemical and fluorescence sensors, emphasizing their superior sensitivity and selectivity in detecting metal ions, such as Pb²⁺, Cd²⁺, and Hg²⁺, even in complex matrices. The key focus of this review is on the use of molecular dynamics (MD) simulations to understand and predict ion transport through graphene membranes, offering insights into their mechanisms and efficiency in removing contaminants. Particularly, this article reviews the effects of external conditions, pore radius, functionalization, and multilayers on water purification to provide comprehensive insights into filtration membrane design. Functionalized graphene membranes exhibit enhanced ion rejection through tailored electrostatic interactions and size exclusion effects, achieving up to 100% rejection rates for selected heavy metals. Multilayered and hybrid graphene composites further improve filtration performance and structural stability, enabling sustainable, large-scale water purification. However, challenges related to fabrication scalability, environmental impact, and cost remain. This review also highlights the importance of computational approaches and innovative material designs in overcoming these barriers, paving the way for future breakthroughs in graphene-based filtration technologies.