In numerous industrial applications, the microstructure of materials is critical for performance. However, finite element models tend to average out the microstructure. Hence, finite element simulations are often unsuitable for optimisation of the microstructure. The present paper presents a modelling technique that addresses this limitation for superabsorbent polymers with a partially cross-linked surface layer. These are widely used in the industry for a variety of functions. Different designs of the cross-linked layer have different material properties, influencing the performance of the hydrogel. In this work, the effects of intrinsic properties on the fracture nucleation and propagation in cross-linked hydrogels are studied. The numerical implementation for crack propagation and nucleation is based on the framework of the extended finite element method and the enhanced local pressure model to capture the pressure difference and fluid flow between the crack and the hydrogel, and coupled with the cohesive method to achieve crack propagation without re-meshing. Two groups of numerical examples are given: (1) effects on crack propagation, and (2) effects on crack nucleation. Within each example, we studied the effects of the stiffness (shear modulus) and ultimate strength of the material separately. Simulations demonstrate that the crack behaviour is influenced by the intrinsic properties of the hydrogel, which gives numerical support for the structural design of the cross-linked hydrogel.