We have used full-atomistic molecular dynamics (MD) simulations of both random and blocky sequence hydrogel networks of poly(N-vinyl-2-pyrrolidone-co-2-hydroxyethyl methacrylate) (P(VP-co-HEMA)) with a composition of VP/HEMA = 37:13 to investigate the effect of the monomeric sequence and the water content on the transport properties of ascorbic acid and D-glucose at 310.15 K. The degrees of randomness of the monomer sequence for the random and the blocky copolymers were 1.170 and 0.104, respectively, and the degree of polymerization was fixed at 50. By analyzing the pair correlation functions, it was found that for both monomeric sequences, the guest molecules (i.e., ascorbic acid and D-glucose) have greater accessibility to the VP units than to the HEMA units due to the higher hydrophilicity of VP compared to HEMA units. While the monomeric sequence effect on the P(VPco-HEMA) hydrogel is clearly observed with 20 wt. % water content, the effect is significantly reduced with 40 wt. % water content and disappears completely with 80 wt. % water content. This is because the hydrophilic guest molecules are more likely to be associated with water molecules than with the polymer network at the high water content. By analyzing the diffusion of the guest molecules and the inner-surface area, it is also found that the guest molecules are confined in the system at 20 wt. % water content, resulting in highly anomalous sub-diffusion. Therefore, at low water content, the diffusion of the guest molecules in the hydrogel is directly affected by the monomeric sequence through the interaction of guest molecules with the monomeric units, whereas such monomeric sequence effects are significantly reduced with increasing water content.