Surface capped copper sulfide nano-aquaformulations were prepared by in situ combination of copper ions with sulfide ions using sonochemical method, followed by microwave irradiations, in the presence of capping agents. Prepared nano-aquaformulations were characterized for particle size, morphology and optical properties. The in vitro antifungal evaluations studies indicated multifold efficacy against Alternaria alternata, Drechslera oryzae and Curvularia lunata in comparison to standard used. The in vivo seed treatment on discoloured paddy seeds showed the optimum results on application @ 7μg/ml for 2 h in case of citrate capped copper sulfide nanoformulation (NCuS3). Significant reduction in seed rot and seedling blight was observed with favourable effect on germination and growth parameters at this concentration.