Forest ecology has significant potential for carbon (C) and heavy-metals’ accumulation, and is considered important for mitigating environmental impacts within the ecosystem. Heavy-metals enter the soil–plant system via different anthropogenic activities per se industrialization, which has huge contribution through the discharge of heavy-metals enriched effluents. Although, irrigation with effluents to large biomass producing forestry plantation e.g. Eucalyptus sp. with high net primary production (NPP) are considered ecologically and environmentally safe, yet the information on differential response of diverse clones towards applied effluents is scares. We therefore, performed field evaluation of nine Eucalyptus clones originated from diverse agro-ecological environments irrigated with distillery effluents to investigate their growth attributes, heavy-metals (e.g. As, Cr, Cd and Ni) and micro-nutrients (e.g. Cu, Zn, Fe and Mn) uptake potential, and C storage in above-and below-ground biomass and sequestration in soil C pool. The diameter at breast height (DBH), tree volume, fresh and dry biomass of stems, leaves, branches and roots of C-316 clone was significantly (p < 0.05) higher, lowest for PE-6, whilst the C-411, C-2045, PE-5, PE-7, PE-8, PE-11 and C-413 were in-between. The Cr uptake was significantly higher for PE-8 and C-413, Ni uptake in PE-6 and C-413 and Pb uptake in clone C-2045. Among micro-nutrients, Zn, Mn and Fe uptake was significantly higher for C-316, compared with other clones. However, the metal content in surface (0–15 cm) soil layer was well below the threshold level. The partitioning of NPP among different above-and below-ground biomass components revealed that dry stem biomass comprised ~ 54.8–56.7%, branches ~ 15.8–17.1%, while leaves ~ 5.6–7.5% of total dry tree biomass. Root biomass comprised ~ 21.3% of total tree biomass. Carbon stocks in dry above-ground biomass (stems + branches + leaves) varied between 33.9 and 59.5 kg C tree−1, and were significantly higher for C-316, and lowest for PE-6 clones. The total C sequestration in tree biomass varied between 229.7 and 450.9 Mg C ha−1 in different clones; with significantly higher in C-316 and lowest in PE-6. Carbon sequestration rate varied between 57.4 and 112.7 Mg C ha−1 year−1 for different Eucalyptus clones. Total organic C (TOC) stocks in surface soil layer under C-413, C-411 and C-316 clones were significantly (p < 0.05) higher than others. The discriminant function analysis (DFA) showed that two significant canonical discriminant functions (DFs) viz. DF-1 and DF-2 involving total tree biomass, total uptake of As, Pb, Zn, Mn and Fe in above-ground biomass of Eucalyptus clones distinguished different cones, appropriately grouping 97.5% of the tested clones. These results underpin overwhelming significance of C-316 plantation for increased heavy-metals’ uptake with co-benefits of C sequestration in tree biomass as well as in soils. Therefore, a stringent policy framework for large scale C-316 clone plantation in regions with availability of distillery effluents is required for restoring the forest ecosystem on sustainability basis.