You have to modify the projection matrix to account for the aspect ratio.
If you haven't yet manipulated the projection matrix (which means you are using an orthographic projection) and are using the fixed-function pipeline, then the easiest solution is to add the following in your render loop before your rendering (or just when the window changes in size):
float aspect = (float)windowWidth/windowHeight;
GL11.glLoadIdentity();
GL11.glOrtho(-aspect, aspect, -1, 1, -1, 1);
or equivalently:
float aspect = (float)windowWidth/windowHeight;
GL11.glLoadIdentity();
GL11.glScale(1.0f/aspect, 1, 1);