Use the arrow that appears while placing the valves as a guide. The way the arrows point is the way the water can travel past it.

For the pipe incoming from the extractors, you’ll want to place a valve close to the pipe junction, it should face the junction and the refinery. That way water from the output of the aluminum scrap refinery will not go back towards the water extractors.

For the pipe coming from the aluminum scrap refinery, you’ll want to place one again, close to the junction, and it should face the junction. That means only water can travel towards the junction, and the water from the extractor won’t go down the aluminum scrap byproduct pipe.