Nanoparticles and metals increasingly intersect with biological systems, demanding biomarkers that are mechanistically informative, field-deployable, and interpretable across species. Framed within a One-Health perspective, this literature review synthesizes evidence on the nano–bio interface from molecular to ecosystem scales. We first situate exposure pathways, environmental fate, and bioavailability highlighting agglomeration, protein corona dynamics, dissolution/redox cycling, and uptake routes that condition internal doses. We then map mechanistic cascades (oxidative stress, immune modulation, genotoxic/epigenetic regulation, tissue injury/repair) onto Adverse Outcome Pathways (AOPs) to clarify where biomarker families read out along the continuum from initiating events to organismal and population effects. Assay domains are examined comparatively: enzymatic/biochemical markers (e.g., CAT, SOD, GPx, LPO), miRNA and broader omics (transcriptomic/proteomic/metabolomic pathways), histopathology and digital pathology, behavioral/physiological endpoints, and environmental DNA (eDNA) biosurveillance. Cross-taxa synthesis spans aquatic vertebrates and invertebrates, amphibians/reptiles, and birds/mammals, distilling concordance/discordance patterns among endpoints and contexts. For multimodal inference, we review Weight-of-Evidence, multivariate panel construction (PCA/PLS/clustering), and probabilistic/Bayesian fusion with attention to calibration and uncertainty. Quality and standards are emphasized (controls, effect sizes, MIQE/FAIR/GLP elements) alongside nano/metal-specific interferences and key confounders (life stage, genotype, co-stressors, matrix effects, particle traits/metal speciation). Applications span aquaculture health, wildlife conservation, environmental compliance, and translational/clinical monitoring. We identify critical gaps—chronic low-dose and mixture exposures, under-studied taxa/ecosystems, longitudinal field realism—and propose minimal core panels for lab screening and field deployment, plus a staged roadmap for method harmonization, reference materials, and open data resources. Collectively, the review outlines a path to robust, cross-taxa biomarker architectures that strengthen nanotoxicology inference and One-Health decision-making.