In order to examine the toxic effect of heavy metals (cadmium and nickel) on morpho-anatomy and physiology of two macrphytes Pistia stratiotes L. and Eichhornia crassipes (Mart.) Solms have been collected randomly from contaminated waters. Plants of both species were subjected to metals (Cd, Ni and combination of Cd+Ni) stress. The levels for Cd2+, Ni2+ and Cd2++Ni2+ combined was 0, 50, 100 and 150 mg/L in aqueous medium. The data was recorded for different morpho-physiological and anatomical attributes. The growth of the both plant species was reduced under metal stress. A significant reduction in photosynthetic parameters was noted in E. crassipes and P. stratiotes under metal stress. Organic osmolytes generally increased by metal stress however, E. crassipes accumulated proline and total proteins in higher amount under Ni stress while P. stratiotes showed same response under Cd stress. Ions like K+ and Ca2+ were severely affected by both metals in E. crassipes. Metals improved uptake of both Ca2+ and K+ in shoot and roots under metal stress in P. stratiotes. However Na+ and Cl- was not affected by metal stress. E. crassipes is better accumulator of both Ni and Cd however; Ni in root was more in P. stratiotes when applied in combination with Cd. Root area, root pith area and pith cell area, root xylem area, metaxylem area and endodermal cell area generally increased in E. crassipes under metal stress. Root epidermal cell area, cortical region cell area and its thickness and aerenchymatous area increased in both P. stratiotes and E. crassipes under metal stress. However, phloem area increased only in P. stratiotes under all stresses. Leaf anatomical characteristics like adaxial or abaxial epidermal cell area were relatively more responsive to Cd stress when applied alone or in combination with Ni in P. stratiotes. However, trichome number and length increased at lower levels of stress in P. stratiotes. Stomatal density on both leaf surfaces and bundle sheath cell area generally increased in E. crassipes under metal stress. Other leaf characteristics like aerenchymatous area, vascular bundle area, stomatal area, sclerenchyma area, chlorenchymatous area, xylem area, phloem area and lamina thickness generally decreased under metal stress. It is concluded thatE. crassipes is relatively more sensitive to Cd than Ni, whereas P. stratiotes is more sensitive to Ni than Cd. Both species are metal accumulators and can be used for phytoremediation of metal effected soils and water.