Studying the impact of residual soil nanomaterials is a promising challenge for sustainable agricultural development to improve soil health and crop productivity. The objective of this study is to assess the long-term impacts of 50, 100, and 250 mg kg−1 soil of nanobiochar (nB) and nano-water treatment residues (nWTR) on the fertility, biological activity, and yield of maize (Zea mays L.) growing in heavy metal-contaminated soils. The results showed that when nB and nWTR were added in larger quantities, the concentrations of lead (Pb), nickel (Ni), cadmium (Cd), and cobalt (Co) extracted with DTPA decreased. With the addition of nB or nWTR, it also showed a significant increase in exchangeable cations, cation exchange capacity (CEC), soil fertility, soil organic matter (OM), microbial biomass carbon (MBC), and a decrease in soil salinity and sodicity. Catalase and dehydrogenase activities rose as nB addition increased, while they decreased when nWTR addition increased. In comparison to the control, the addition of nB and nWTR greatly boosted maize yield by 54.5–61.4% and 61.9–71.4%, respectively. These findings suggest that the researched nanomaterials’ residual effect provides an eco-friendly farming method to enhance the qualities of damaged soils and boost maize production. Our research suggested that adding recycling waste in the form of nanoparticles could immobilize heavy metals, improve soil characteristics, and increase the soil’s capacity for productivity.