Pit lakes are artificial hydrological features created by mining operations that typically suffer from acid mine drainage (AMD), which not only endangers water quality but also exacerbates carbon loss. However, the impacts of AMD on the fate and role of dissolved organic matter (DOM) in pit lakes remain unclear. This study employed negative electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) combined with biogeochemical analysis to examine DOM molecular variations and environmental controls across the AMD-induced acidic and metalliferous gradients in five pit lakes. The results demonstrated distinct DOM pools in pit lakes characterized by the prevalence of smaller aliphatic compounds compared to other waterbodies. AMD-induced geochemical gradients promoted DOM heterogeneity among pit lakes, with acidic pit lakes containing more lipid-like compounds. Acidity and metals enhanced DOM photodegradation, reducing the content, chemo-diversity and aromaticity. Organic sulfur was detected in high abundance, potentially from sulfate photo-esterification and mineral flotation agent. Furthermore, microbial involvements in carbon cycling were revealed by DOM-microbe correlation network, but microbial contributions to the DOM pools decreased under acidic and metal stresses. These findings highlight abnormal carbon dynamics caused by AMD pollution and integrate DOM fate into pit lake biogeochemistry, thereby contributing to management and remediation.