Rapid, uneven urbanisation of Varanasi — a Ganga-riverine city that carries some of the heaviest vehicular, industrial and biomass-combustion loads in the middle Indo-Gangetic Plain 11–17 — has created a fine-grained mosaic of pollution intensities within a few kilometres of one another. Indigenous medicinal herbs growing along this gradient (e.g., Ocimum tenuiflorum L., Withania somnifera (L.) Dunal, Azadirachta indica A. Juss., Adhatoda vasica Nees and Aloe vera (L.) Burm.f.) are simultaneously culturally valued, pharmacologically important, and physiologically exposed sentinels of ambient stress. This paper (i) synthesises current, peer-reviewed evidence on how urban abiotic stressors — particulate matter, ground-level ozone, heavy-metal deposition and elevated ambient temperature — reshape the phenylpropanoid, flavonoid, alkaloid and terpenoid pools of medicinal plants 1–10,18–24, and (ii) presents a field-validated, top-journal-grade methodological protocol designed specifically for a four-zone urban stress gradient in Varanasi (heavy-traffic core, mixed residential–commercial, institutional/green-belt, and peri-urban reference sites). The protocol integrates a multi-marker biochemical battery (total phenolics, total flavonoids, total alkaloids, tannins, proline, and malondialdehyde and antioxidant enzyme activity) with instrumental fingerprinting (UV-Vis spectrophotometry, HPLC and GC-MS) and rigorous statistical validation (ANOVA with Tukey's HSD, Pearson/Spearman correlation with AQI and PM2.5, and multivariate ordination). Drawing on comparable Indo-Gangetic studies, we outline the anticipated direction and magnitude of metabolite shifts across the gradient and discuss their implications for the phytochemical quality, safety and standardisation of herbal raw material sourced from urban and peri-urban tracts. The framework is intended to generate the first systematic, site-resolved phytochemical stress map for medicinal flora of the Varanasi urban agglomeration.