Gold nanoparticles (AuNPs) protected by a grafted ligand monolayer are commonly used for applications in biosensing, bioimaging, and drug delivery, in part because of the ability to tune surface properties by modifying the composition of the protecting ligands. If the surface monolayer contains multiple distinct ligand species, the AuNPs are referred to as mixed-monolayer-protected particles. A typical mixed monolayer consists of two linear alkanethiol ligands, with one ligand species end-functionalized to confer aqueous solubility. However, the inclusion of multiple ligand species raises questions of how the nanoscale morphology and the relative lengths of the two ligands can affect properties, considerations that are unnecessary for single-component monolayers. In this work, we use atomistic molecular dynamics simulations to model the structure of mixed-monolayer-protected AuNPs in aqueous salt solution under typical biological conditions. We focus on identifying changes in the monolayer structure as a function of the diameter of the AuNP core, the morphology of the protecting ligands, and the relative ligand length, complementing existing studies of homogeneous monolayers. Our results show that increasing the particle diameter strongly inhibits ligand fluctuations, consistent with a reduction in free volume associated with higher-curvature substrates. We also show that, in aqueous solution, particles with striped, mixed, and random morphologies exhibit similar behaviors, as ligand fluctuations mask any influence of the grafting positions. Finally, our simulations indicate that long hydrophobic ligands always deform to allow shorter hydrophilic ligands to access water, leading to a significant distortion of the interface if the hydrophobic ligands are much longer than the hydrophilic ones. Our results thus provide new physical insight into the structure of mixed-monolayer-protected particles under typical biological conditions and can be used to guide the experimental design of new classes of AuNPs for biological applications.