I had a similar Idea I never actually attempted (although it is still in the pipeline) the timing of the pumping would be that hard part and would possibly require some custom curcuitry to get an even tidal flow.
My idea also incorporated a third tank as a refugium/sump to increase the water volume etc... so the water pumped from one tank through the refugium and out into the third. each tank would also require a filtration system in the deeper end.
I also worked out that the tanks would need to be a minimum of 600mm high (preferably 800 or more) to get any major benefits of doing the tidal flow. (tidal flows affect more than just the surface of the sand, there needs to be a fair amount of subsurface drainage to allow the natural ecology to occur, my tests (sound very scientific doesn't it, involved a bit of digging at different tides and seeing how long it took to get much seepage) in the mudflats off Matua showed the average drainage needs to be around 150 -200mm deep, add that to how much you want it covered by at "high tide" and how much you want left at "low tide" and you see the issue.