Due to the vast extent of desert areas in Iran, where the water shortage crisis poses a serious challenge to sustainable development, the optimal use of non-conventional water resources, including wastewater, has become increasingly important. The growth of industrial activities and the direct discharge of contaminated effluents into water bodies not only intensify water scarcity, but also lead to extensive environmental pollution. Among various treatment technologies, adsorption is considered one of the most efficient methods for removing dye pollutants. The use of natural adsorbents has attracted particular attention due to their environmental compatibility. In the present study, the ability of the biomass of the native and drought-tolerant plant Peganum harmala L. to remove methylene blue dye from wastewater was investigated, as a step toward the sustainable utilization of unconventional water resources. The effects of several factors, including adsorbent dosage (0.01–0.08 g), contact time (5–15 min), initial dye concentration (10–35 mg/L), and initial pH (2–12), were examined. Under optimal conditions of pH = 7, contact time of 13 min, adsorbent dosage of 0.06 g, and an initial dye concentration of 10 mg/L, the removal efficiency of methylene blue was about 92%. Isotherm studies indicated that adsorption fitted well with the Langmuir isotherm, with a maximum adsorption capacity of 59 mg/g, and the adsorption process followed the pseudo-second-order kinetic model with an R² value of 0.9872. The calculated Gibbs free energy changes (ΔG°) at 15°C (–39.65 kJ/mol), 20°C (–40.37 kJ/mol), 25°C (–40.51 kJ/mol), and 30°C (–41.05 kJ/mol) indicated that the adsorption process was spontaneous. Therefore, the use of Peganum harmala biomass as an environmentally friendly adsorbent represents an effective approach for the removal of methylene blue dye. Under optimal conditions, this plant offers significant efficiency in wastewater treatment, which can help reduce pressure on freshwater resources, protect fragile desert ecosystems, and provide a sustainable and cost-effective solution for water management in arid regions.