Antennas can be mounted vertically or horizontally but the orientation of the tag to the loop is significant. Pass-through is the best orientation since the coil in the tag is the same as the antenna loop. The tag reads the best when it is directly out from the center of the loop where the charge field is strongest.
Pass-over/pass-by antennas put the tag coil at 90 degrees from the loop plane. In this orientation tags will be detected best when they are over the wire so two separate detections per pass are possible. The magnetic charge is not as strong with this orientation so the read range will usually be less than with a pass-through antenna.
Hybrid antennas have been constructed by mounting the antenna in a rigid structure and attaching the bottom to the stream bottom with a hinge. At low flows the antenna is passover/passby and the antenna will float to a vertical position when there is sufficient water flow.
Though the read range can be degraded when metal is nearby, it can often give acceptable performance. There are techniques that can be used to minimize the effect. Contact Oregon RFID tech support if you need to place antennas near metal.