Chitosan is a versatile biopolymer that can self-assemble in solution to form hydrogels and nanoparticles. It consists of two types of monomers: glucosamine (GlcN) and N-acetylglucosamine (GlcNAc). Chitosan self-assembly is controlled by a balance of interactions between these two types of monomers: GlcN which gets protonated in solution leading to electrostatic repulsion and GlcNAc which contains an acetyl group, leading to hydrophobic and hydrogen bonding interactions. We present the results of discontinuous molecular dynamics (DMD) simulations aimed at understanding how the degree of acetylation (DA) and monomer sequence affect network formation in solution. Chitosans with DAs ranging from 10% to 50% and three different monomer sequences random, evenly spaced, and blocky are studied. We show that chitosans with blocky sequences of GlcNAc monomers form percolated networks earlier in time than random and evenly spaced sequences for all DAs tested. Analysis of the pore size distributions of the resulting chitosan networks shows that blocky sequences of GlcNAc monomers lead to larger pores than random and evenly spaced sequences for DAs less than or equal to 30%. The monomer sequence has little impact on pore size distribution when the DA is 40% or higher. Finally, we show that at low DA, chitosan networks allow free diffusion of small molecules through the network but slow the diffusion of large molecules. At high DA, chitosan networks allow free diffusion of both large and small molecules. We conclude that controlling the monomer sequence of chitosan could be effective at controlling the structure of the resulting network.