How to implement this kind of ripples with a GLSL fragment shader?

I tried to implement what teodron suggested:

void main()
{
    vec2 uv = gl_FragCoord.xy / resolution.xy;
    float sepoffset = 0.005*cos(iGlobalTime*3.0);
    if (uv.y > 0.3 + sepoffset)// is air - no reflection or effect
    {
        gl_FragColor = texture2D(texture, vec2(uv.x, -uv.y));
    }
    else
    {
        // Compute the mirror effect.
        float xoffset = 0.005*cos(iGlobalTime*3.0+200.0*uv.y);
        //float yoffset = 0.05*(1.0+cos(iGlobalTime*3.0+50.0*uv.y));
        float yoffset = ((0.3 - uv.y)/0.3) * 0.05*(1.0+cos(iGlobalTime*3.0+50.0*uv.y));
        vec4 color = texture2D(texture, vec2(uv.x+xoffset , -1.0*(0.6 - uv.y+ yoffset)));
        // 
        //vec4 finalColor = vec4(mix(color.rgb, overlayColor, 0.25), 1.0);
        gl_FragColor = color;
    }
}

It looks pretty close (it's hard to tell without the base image) but you can tweak the parameters.

You may see it in action there: https://www.shadertoy.com/view/Xll3R7

Some remarks:

• I had to invert the y coordinate since I was getting the image upside down, but it may depend of what you pass into resolution.xy; if the result is inverted for you, just uninvert uv.y
• I changed your uniform declarations so it works with shadertoy. You can ignore those changes.
• You will need however to add a uniform providing the time and use it in place of iGlobalTime (which is the time in seconds)
• I added a tide effect since it looks like there is one on your example but it's hard to tell (see sepoffset variable). You may remove it if you don't like it
• I removed the overlay color since it was not looking good, and your example didn't had one
• To tweak the effect to your taste:
  • change the factor of iGlobalTime to speedup/slowdown the effect (you can change each of them separately if you want, let's say accelerate the x movement and slow down the y movement)
  • change the cos() factor to amplify/attenuate the effect

EDIT: I changed the yoffset to include the modification from @cepro