In this work, the hetero-aggregation behaviour of well-characterized copper nanoparticles (Cu-Nps) prepared by Koelreuteria apiculata seed extract, was investigated on the soil via sorption studies. Fate on sand was determined by the introduction of suspended particles in the form of pulse in Plexiglas column packed with fully saturated sand. Photo-degradation study was conducted in visible light for ensuring the stability of the formed Cu-Nps. For ensuring their biological incongruity, the effect of Cu-Nps were investigated against Staphylococcus aureus, Escherichia coli, and Salmonella typhi. The antifungal activity was manoeuvred on Laurilia taxodi for manifesting its status against fungal community. The impact of Cu-Nps on Chlorella sp. was ameliorated with the increasing chlorophyll content from 34% to 43% with the concentrations of 100 mg/L to 5000 mg/L respectively. The genetic effect of 2500 mg/L of Cu-Nps was divulged to be nearly negligible with the value of 0.004 as chromosomal aberration index, on the newly emerged root tips of Allium cepa. Cu-Nps played a pivotal role in enhancing chlorophyll accumulation and enzymatic activity in the seeds of Cicer arietinum with the 100% germination rate. All the studies covering biotic and abiotic parameters inferred the biocompatible nature of the Cu-Nps beforehand, thus paving their way to nature without any disquiet regarding their detrimental temperament.