A window assembly heat transfer system is disclosed in which a window member has a selected transparency to monitored or sensed electromagnetic wavelengths. One or more passages are provided in the window member for flowing a single-phase or two-phase heat transfer fluid. A mechanism allows either evaporation or condensation of the fluid and/or balancing of a flow of the fluid within the passages. In one embodiment, the window assembly can be made by producing passages in a top surface of a first single plate, optionally producing passages in a bottom surface of a second single plate and bonding the top surface of the first plate to a bottom surface of a second single plate to form the window member with the passage or passages. In another embodiment, the window assembly can be made by providing a core around which the window member material is grown and thereafter removing the core to produce the passage or passages.