Does your design have to hold water perfectly, or can it leak a little water? For example, is there some rate of water flow out of the wetland, so if you restrict the water flow to a trickle at the stop logs, then that will manage the water level in the wetland? (Good is MUCH easier than perfect.)
Tinylake operates a similar system of stop logs so I would heed his advice. I think his most important advice is that the boards will swell as they absorb water!
I also agree with the ship lap joints, that should significantly reduce your water flow through the boards.
Finally, you do NOT need your stop boards to match your groove thickness. Get the most readily available thickness that will serve your purpose. (Probably 1-3/4" thick. Does Canadian dimensional lumber match U.S. dimensional lumber, but just measured in metric?)
After your install your stop boards, you can then just hold them in place with your "pin board". (Sorry, I can't remember the correct name.) Get that piece to the correct thickness to also fit inside your grooves with a little gap. Turn that board so that the long dimension is vertical and it can pin all of your stop boards in place! (It should be a little higher than your highest stop board when installed.) Then pound in two wedges to hold it in place like Tinylake's picture.
The top wedge needs to be ABOVE the water level at full pool. For removal, you can then easily knock out the top wedge and then wiggle the pin board to loosen the bottom wedge.
P.S. If there can be zero trickle, then you may need to make your board dimensions a little smaller and put some compressible rubber(?) material between the stop boards and the downstream edge of the groove, so it will really seal when all of your boards are wedged into place.
Good luck on your managed wetlands project!
