The characterization, adsorption mechanisms, and process-influencing aspects of nanoparticles made from agricultural waste are the main topics of this review, which focuses on the adsorption of methylene blue (MB). Key functional groups (O–H, C = O, and Fe–O) that aid in MB adsorption are revealed by Fourier Transform Infrared (FTIR) spectroscopy; shifts in this spectroscopy indicate active interactions. ZrO₂ nanoparticles from Sapindus mukorossi extract exhibit high crystallinity and enhanced adsorption, which is confirmed by X-ray diffraction (XRD), which also increases adsorption efficiency. Energy Dispersive X-ray Spectroscopy (EDX) and Scanning Electron Microscopy (SEM) show improved MB removal with functionalization and pore filling, and they offer insights into the surface shape, content, and adsorption efficacy of nanoparticles. Adsorption is greatly influenced by pH and Zero Point Charge (ZPC), with alkaline circumstances (pH 10) optimizing MB removal because of the electrostatic interaction between the negatively charged nanoparticle surface and positively charged MB dye. The process’ spontaneity and favourability are demonstrated by adsorption kinetics, thermodynamics, and isotherms (Langmuir, Freundlich); removal efficiency increases with increased pH and suitable doses. Another important factor is temperature, which improves absorption through better diffusion and higher kinetic energy. Nanoparticle porosity is measured using Brunauer–Emmett–Teller (BET) surface area analysis. Nanoparticles generated from eucalyptus residue have the largest specific surface area (1144.56 m2/g), which maximizes MB adsorption. This review emphasizes the effectiveness, affordability, and accessibility of nanoparticles obtained from agricultural waste for the effective removal of MB in wastewater treatment.