Abstract: The waterproof performance, mechanical properties, chemical composition, microstructure, and pore structure of hydrophobically-modified geopolymer concrete are investigated before and after dry-wet cycles, to determine the long-term feasibility of using hydrophobically-modified geopolymer concrete in wet environments. We use two types of organic modifying agents: polydimethylsiloxane (PDMS) and sodium methyl siliconate (SMS). The experimental results show that incorporating 2%–6% PDMS or 5%–15% SMS can make the concrete hydrophobic, with water absorption and chloride transport rates decreasing by up to 94.3%. We also analyze the bonding modes of organic molecules and geopolymer gels, as well as their evolution mechanisms during dry-wet cycles. PDMS-modified geopolymer concrete is found to exhibit long-term waterproof performance that is not weakened by dry-wet cycles. This is attributed to the robust combination of organic components and the geopolymer gel skeleton formed through phase cross-linking. Meanwhile, PDMS-modified geopolymer concrete’s hydrophobicity, strength, and microstructure are essentially unaffected. In contrast, SMS-modified geopolymer concrete shows higher water sensitivity, although it does maintain efficient waterproof performance. Due to relatively low binding energy, the dry-wet cycles may lead to the detachment of some SMS molecules from the gel network, which results in a decrease of 18.6% in compressive strength and an increase of 37.6% in total porosity. This work confirms the utility of hydrophobically-modified geopolymer concrete as a building material for long-term service in wet environments, for instance areas with frequent precipitation, or splash and tidal zones.