High-density polyethylene (HDPE) waste and chicken eggshell were used to synthesize three novel adsorbents, namely mesoporous graphene (MG), nano-eggshell modified graphene (nEMG), and nano-magnetic eggshell modified graphene (nM-EMG) for methyl red (MR) adsorption from simulated wastewater. The effects of adsorption conditions (pH, contact time, initial dye concentration, adsorbent dose, and temperature) were investigated. MG, nEMG, and nM-EMG were characterized using SEM, TEM, BET, EDX, XRD, and FTIR analyses. MG, nEMG, and nM-EMG had specific surface areas of 15, 31, and 179 m2/g and mean pore diameters of 27, 29, and 5 nm respectively. The equilibrium adsorption capacities of MG, nEMG, and nM-EMG were 5.6, 8.1, and 6.5 mg/g respectively at MR concentration of 100 mg/L, pH 4, adsorbent dose of 1.0 g/100 mL, and temperature of 25 °C. All MR sorption processes followed the pseudo-second-order and Langmuir–Freundlich model. The adsorption rates were controlled by intra-particle and film diffusion. MR uptake on the synthesized adsorbents was spontaneous, endothermic, and chemisorption. The adsorption occurred via electrostatic interactions, π electron interactions, and hydrogen bonding. The performance of the prepared adsorbents was examined in different water matrices and compared with other MR adsorbents. After five regeneration cycles, the adsorbent reusability study showed that nM-EMG is the most stable and reusable adsorbent.