With the increasing needs of clean water supplies, the use of biomass wastes and residues for environmental remediation is essential for environmental sustainability. In this study, the residues from winery and citrus juice industries, namely grape skin and orange peel, respectively, were first converted to hydrochars by hydrothermal carbonization (HTC) and then a cationic dye (methylene blue) adsorption was studied on hydrochars. Hydrochars from both feedstocks were produced at three different temperatures (180, 220, and 250 °C) and a fixed residence time (1 h) to evaluate the hydrochar’s performance on the dye adsorption. The hydrochars were characterized in terms of their pH, pH at point of zero charge (pHPZC), surface functionalities, and surface area. A batch adsorption study of the dye was carried out with variable adsorbate concentration, pH, and temperature. Two adsorption isotherms namely Langmuir and Freundlich models were fitted at 4, 20, and 36 °C. The thermodynamic properties of adsorption (Gibbs free energy (ΔG), enthalpy (ΔH) and entropy (ΔS)) were evaluated from the isotherms fittings. Results showed that the dye adsorption on both hydrochars was significant and followed Langmuir isotherm. The maximum adsorption capacity on citrus waste hydrochar was higher than the winery waste hydrochar at any corresponding HTC temperature. Although hydrochars showed the lowest surface area (46.16 ± 0.11 and 34.08 ± 1.23 m2/g for citrus and winery wastes, respectively) at 180 °C, their adsorption was the highest, owing to their maximum density of total oxygen functional groups (23.24 ± 0.22 and 32.69 ± 1.39 µmol/m2 for citrus and winery wastes, respectively), which decreased with the increase in HTC temperature. This research shows a sustainable route for the production of highly effective adsorbent materials at lower HTC temperatures from citrus and winery wastes.