You're probably using PulseAudio somewhere in the audio stack. It can select the default output and input device. I think that many environments will have a speaker icon or something in the taskbar.
I just run pavucontrol
directly. Jump over to the "input devices" tab, and you can check the device you want to be an input.
EDIT: If you're using KDE, might be some Qt-based analog -- pavucontrol
uses GTK -- but I don't know the name off the top of my head.