The blood-aqueous barrier is located in the nonpigmented cells of the ciliary epithelium.

The ciliary epithelium consists of the pigmented layer which is located on the stromal side and the nonpigmented layer that faces the posterior chamber. The blood-aqueous barrier is located on the nonpigmented layer. These cells are connected by tight junctions of the leaky type. However, they do not form a solid barrier allowing some protein to pass from the ciliary processes into the posterior chamber.

The blood-retinal barrier and the blood-aqueous barrier appear to overlap in the pars plana.

The blood-aqueous barrier prevents the movement of intermediate- and high molecular weight substances into the posterior chamber, while other substances are actively transported into the posterior chamber and establish osmotic gradient. Breakdown of the blood aqueous barrier reduces the efficiency of the osmotic gradient, which leads to a reduction in aqueous flow.