No, water will not fill a balloon under pressure if it is underwater. The reason is that the pressure inside the balloon will be equalized with the external water pressure. When a balloon is submerged underwater, the pressure exerted by the water increases with depth due to the weight of the water column above it.
If you were to fill a balloon with air and then submerge it, the pressure inside the balloon would remain relatively constant, while the external water pressure would increase with depth. The balloon would experience a force pushing inward from the water, compressing the air inside. However, since the balloon is elastic, it would also exert an outward force resisting the compression. As a result, the pressure inside the balloon would eventually reach equilibrium with the water pressure, and no significant amount of water would enter the balloon.
If you want to fill a balloon with water underwater, you would need to introduce the water directly into the balloon by, for example, using a syringe or some other means of injecting the water.