<p>Ligninolytic enzymes such as laccase, manganese peroxidase (MnP), and lignin peroxidase (LiP) are vital biocatalysts directly involved in the oxidative breakdown of lignin and aromatic pollutants across terrestrial and aquatic systems. Beyond their traditional role in recalcitrant degradation, these enzymes can also function in mediating carbon mineralization, nutrient mobilization, and redox-sensitive metal cycling. Catalytic activity of ligninolytic enzymes is highly responsive to geochemical parameters such as pH, redox potential, and metal ion availability, particularly under fluctuating oxygen conditions common in peatlands, coal seams, and permafrost regions. This study covers the diversity, distribution, and regulation of ligninolytic enzymes across natural environments, sharing insights into their molecular structure, cofactor dependencies, and environmental stability. Emphasis is placed on redox regulation during drought rewetting and freeze–thaw events, which modulate enzyme expression and influence soil organic carbon turnover. Furthermore, potential applications such as degradation of synthetic pollutants, polycyclic aromatic hydrocarbons (PAHs), azo dyes, and nanomaterials is discussed in the context of green remediation. Recent advances in enzyme immobilization, rare earth element stabilization, and bioreactor applications are also highlighted. By integrating microbial enzymology with geochemical processes, this review underscores the multifunctional role of ligninolytic enzymes in mediating carbon cycling, pollutant degradation, and elemental fluxes in stratified ecosystems.</p>