Agricultural runoff rich in nitrogen (N) and phosphorus (P) increasingly threatens water quality in semi-arid regions where water scarcity and land-use intensification coincide. This study compared the phytoremediation efficiency and physiological resilience of Fraxinus (ash) and Juniperus (juniper) under nutrient-enriched conditions, while linking local findings to global evidence on pollutant mitigation and economic co-benefits.Seedlings of both species were cultivated under controlled greenhouse conditions simulating runoff scenarios from the Zayandeh-Rud basin (Iran). Treatments included nitrate (NO₃⁻) and phosphate (PO₄³⁻) enrichment at 0, 5, 10, and 50 mg L⁻¹, replicated three times. Nutrient concentrations were analyzed spectrophotometrically, while physiological traits (chlorophyll content, stomatal conductance, and soil moisture dynamics) were monitored as functional stress indicators. Data were analyzed using repeated-measures ANOVA with Tukey’s HSD post-tests.Both species significantly reduced nutrient concentrations relative to controls (p < 0.05). Fraxinus exhibited higher removal efficiency, achieving up to 46% NO₃⁻ and 33% PO₄³⁻ removal at moderate enrichment (5–10 mg L⁻¹). Juniperus, though less efficient in nutrient uptake (~20–30%), displayed greater physiological stability under stress, with relatively stable chlorophyll and stomatal conductance across treatments. Integration with global datasets revealed complementary roles: evergreen Juniperus accumulates heavy metals (Pb, Zn, Ni, Fe), intercepts particulate matter year-round, and maintains modest but stable biomass (~1.8 t ha⁻¹ yr⁻¹), while deciduous Fraxinus excels in nutrient-rich conditions and demonstrates high foliar metal accumulation indices (MAI ≈ 22–23).These findings highlight a functional complementarity: Fraxinus acts as a fast nutrient sink during runoff peaks, whereas Juniperus provides year-round stabilization through evergreen canopy and pollutant interception. With climate change pushing many temperate and subtropical ecosystems toward semi-arid states, this dual-species palette offers a transferable agroforestry model that enhances water quality, mitigates airborne particulates, and generates medicinal–economic value. Such multifunctional systems can support climate-resilient land management across the Mediterranean, Central Asia, North Africa, and beyond.