Remember the air flow sensor in certain car engines. There is a filament (or film) resistor which is heated by current and cooled by air flow. The flow is measured by measurement the resistance value that depends on the temperature. Use a setup like this. When the fish is passing through the tunnel, it changes the thermal balance inside the tunnel. To simplify the detection, use a set of two similar tunnels and measure the difference (assuming social interaction in fish society is not so advanced so they will not try to fool you by passing both the tunnels simultaneously).