Aquatic environments serve as critical repositories for anthropogenic pollutants and sites of illicit activities, yet traditional chemical and physical forensic methods often struggle with source attribution, temporal resolution, and linkage of evidence to specific actors or events. This comprehensive review examines the emerging integration of forensic botany with aquatic ecology—collectively framed as “green water evidence”—to address these challenges in environmental crime investigation. Drawing on diatom assemblages, phytoplankton communities, macrophytes, bryophytes in wetland margins, environmental DNA (eDNA), stable isotope signatures, and community ecology principles, the review synthesizes how botanical signatures function as persistent, habitat-specific tracers. Key applications include pollution source tracking through indicator species and bioaccumulation patterns that distinguish industrial, agricultural, sewage, and pharmaceutical inputs; reconstruction of illegal disposal events via transferred plant material and sedimentassociated biota on objects, clothing, or vehicles; and broader attribution of environmental crimes such as unauthorized dumping, habitat degradation, and contamination events. Methodological advances—from classical microscopy and acid digestion protocols to DNA metabarcoding, AI-assisted identification, remote sensing of vegetation change, and GIS mapping of ecological fingerprints—are critically evaluated. Case studies illustrate successful linkages of suspects or materials to specific water bodies and the use of plant-based evidence in supporting civil and criminal environmental enforcement. Challenges remain, including spatial-temporal variability of communities, taxonomic expertise gaps, standardization of protocols, and courtroom admissibility. The review concludes that systematic incorporation of aquatic botanical evidence, supported by interdisciplinary collaboration and reference databases, substantially strengthens environmental forensics. Future priorities include expanded eDNA reference libraries, quantitative transfer and persistence studies, integration with chemical forensics, and training for investigators. By treating aquatic plants and algae as silent, ubiquitous witnesses, this integrative approach offers a powerful, underutilized toolkit for detecting, attributing, and deterring environmental crimes that threaten aquatic ecosystems and public health.