Although water is one of the key elements on the globe and accessible in a large amount, nearly one-half of the people of the globe are suffering from a shortage of freshwater that is increasing at a frightening rate, most exclusively in growing nations where commercial water shortages prevail. So, in the regions with ample saline water and solar radiation where freshwater is usually limited, the humidification-dehumidification (H-DH) desalination systems have demonstrated inspiring outcomes. The experimental, theoretical, and economical analysis of the bubble column (BC) humidifier, thermoelectric cooler (TEC) based dehumidifier H-DH system has been presented in this work. The effect of various operational parameters on H-DH systems like Ta, Tw, H, do, and ya has been studied. The daily experimental and theoretical productivity obtained during the analysis of the H-DH system was in the span of 7–13 L/day and 9.1–12.4 L/day, respectively, for dissimilar functional variables while the greatest experimental and theoretical productivity was reported 12.97 L/day and 12.4 L/day, respectively, for do = 2 mm, ya = 0.016 kg/s, Tw = 60 °C, Ta = 27 °C, and H = 7 cm. Also, the experimental results present a fine confirmation with the results of the proposed mathematical model. From the economic analysis, it is found that the yearly price per liter and the payback period of the H-DH system are Rs. 5.1/L and 2.4 years, respectively, which is a very promising value.