Superhydrophobicity is highly desirable for a wide range of applications. However, achieving it on intrinsically hydrophilic substrates without relying on low-surface-energy coatings presents a significant challenge. This study demonstrates a manufacturing solution to this problem by employing two-photon polymerisation (TPP) to create synergistic re-entrant and hierarchical structures that enforce superhydrophobicity through topography alone. Arrays of mushroom-shaped (MS), inverted-crown mushroom (ICM), and multi-crown mushroom (MCM) microstructures were designed and fabricated. The MCM architecture, which incorporates unique secondary pillars atop micro-caps, achieved a contact angle exceeding 150° and a sliding angle less than 10° on a hydrophilic OrmoComp substrate, as verified by XPS analysis. Numerical simulations elucidate that the re-entrant geometry provides energy barriers that stabilise the Cassie–Baxter state, but these barriers become insufficient at inter-structural gaps over 30 μm for MS and ICM. In contrast, the secondary pillar arrays not only minimise solid-liquid contact to achieve a high contact angle, but also introduce additional dragging forces. As a result, the MCM surface sustains the Cassie–Baxter state even at a spacing of 40 μm. This work demonstrates that TPP is a viable manufacturing route for creating topography-driven superhydrophobicity on intrinsically hydrophilic surfaces without chemical modification.