What to do if you have running water coming through the holes
If you have running water coming through the holes, try to wait for a dry spell to do the repair. Some of these hydraulic repair cements will work if there is moving water, but it's not guaranteed.
You don't need to fill the rod hole to its complete depth with the repair material. If you just get it into the hole about 2 inches, that should be plenty.
Once the material hardens after about 30 minutes, try to keep it damp by spritzing the concrete wall around the hole with the spray bottle and clear water. If you can keep the repair compound wet for at least 24 hours or more, it will help create a strong and permanent repair.