Melon by-products, that currently lack high value-added applications, could be a sustainable source of bioactive compounds such as polysaccharides and antioxidants. In this work, melon peels were extracted with water to remove free sugars, and the water-insoluble solids (WISs) were subjected to hydrothermal processing. The effect of temperature on the composition of the obtained liquors and their total phenolic content was evaluated. The selected liquors were also characterized by matrix assisted laser desorption/ionization-time of flight mass spectroscopy (MALDI-TOF MS), fourier transform infrared spectroscopy (FTIR) and high performance anion exchange chromatography with pulsed amperometric detection (HPAEC–PAD), and its phenolic compounds were identified and quantified by high-performance liquid chromatography-diode array detector-tandem mass spectrometry (HPLC–DAD–MS/MS). In addition, the spent solids from the hydrothermal treatment were characterized and their potential use was assessed. At the optimal conditions of 140 °C (severity 2.03), the total oligosaccharide yield accounted for 15.24 g/100 g WIS, of which 10.07 g/100 g WIS were oligogalacturonides. The structural characterization confirmed the presence of partially methyl esterified oligogalacturonides with a wide range of polymerization degrees. After precipitation, 16.59 g/100 g WIS of pectin were recovered, with a galacturonic acid content of 55.41% and high linearity.