The long-term durability of hydraulic concrete infrastructure is severely compromised by water penetration, carbonation, and chloride ion erosion, necessitating the development of high-performance protective coatings. This study designed two polyaspartic ester polyurea coatings, PAE-PTMEG and PAE-PPG, derived from isocyanate prepolymers with polytetramethylene ether glycol (PTMEG) and polypropylene glycol (PPG) soft segments, respectively. The results demonstrated that the PTMEG-based prepolymer exhibited higher reactivity, leading to shorter curing times. The resulting PAE-PTMEG coating showed outstanding mechanical properties (tensile strength: 43.8 Mpa; elongation: 646.1%) and excellent water resistance (<1% absorption), attributable to its well-defined microphase-separated structure. When formulated into a practical paint (PAE-C), it surpassed mechanical standards for waterproofing and demonstrated exceptional resistance to chloride ion penetration (1.3 × 10⁻⁴ mg·cm⁻²·d⁻¹), complete carbonation resistance, and high frost resistance (200 cycles). This work confirms that tailoring the soft segment structure is a crucial strategy for developing durable polyurea coatings, with PAE-PTMEG showing significant potential for protecting critical water conservancy infrastructure.