The objective of this investigation is to assess the performance of various heat exchangers for application in a novel solar-powered zero liquid discharge humidification-dehumidification desalination system. In this study four heat exchangers (HX) having two different flow configurations namely counter flow (cf), cross flow (cr) made up of three different materials namely high-density polyethylene (HDPE), aluminum (Al), and Polypropelyne (PP) were compared in terms of their effectiveness and overall heat transfer coefficient under varying salinity levels (up to 10%) and mixing ratios (0.22–0.45). At a mixing ratio of 0.22 and 0% salinity, PP-HXcr and Al-HXcf exhibited similar effectiveness (∼85%), surpassing that of HDPE-HXcf (∼65%). Despite PP-HXcr's lower thermal conductivity in comparison to Al-HXcf, comparable effectiveness was achieved due to the superior flow distribution in PP-HXcr. Further investigations focused on the impact of salinity on heat exchanger performance. At 3.5% salinity, all heat exchangers experienced a decline in effectiveness and heat transfer coefficient (HTC), with Al-HXcf experiencing a more pronounced decrease compared to PP-HXcr. The higher thermal conductivity of Al-HXcf led to greater salt accumulation, while PP-HXcr demonstrated minimal fouling. As the experiment progressed, fouling increased for all heat exchangers, with the Al-HXcf being practically ineffective at 10% salinity with an effectiveness below 10%. To address the issue of fouling, a rotating cross-flow heat exchanger (RPP-HXcr) was introduced. While the effectiveness of the PP-HXcr drops from 85% to approximately 60% with increasing salinity from 0% to 10%, the RPP-HXcr demonstrates only a marginal decline in effectiveness with increasing salinity. For instance, at mixing ratio of 0.22 when the salinity is increased from 0% to 10%, the effectiveness of RPP-HXcr only drops from 83% to 77%. This exceptional performance was attributed to the continuous contact between the rotating tubes and the incoming feed, effectively preventing fouling and ensuring sustained efficiency. Rotating cross-flow heat exchanger (RPP-HXcr) is introduced and validated as a potentially reliable solution for mitigating fouling, as it demonstrates sustained efficiency and minimal performance degradation across different salinity conditions.