Chinampas design question

First off, what I'm planning to create here are probably not true Chinampas, since the channels will not be filled with water through much of the growing season. That said, I have a seasonal creek that flows through what we could call a seasonal wetland, itself within a rather narrow valley with steep sides. The area is waterlogged through the winter and spring and remains soft during much of the summer. My plan is to dig a series of wide trenches running out from the creek toward the valley edge, using the dirt to build up planting beds in-between the trenches.

My question regards the best orientation of these channels and beds. The three options are to dig the channels perpendicular to the main creek, pointed somewhat downstream, or pointed somewhat upstream. My inclination is to cooperate with nature and angle downstream, but I don't know enough about waterflow patterns to really weigh the advantages and disadvantages. Fwiw, I also plan to put in beaver-analog check dams roughly at the level of each channel.

Any thoughts? Thanks.

I think what you are asking is if you want water to flow "upstream" into your channels or "downstream".

My instinct is to have the channels going against the flow. You don't really want a flow in these channels at all, you just want them to hold and sink some stationary water to irrigate everything. I think if you dug them "down hill" they might turn into actual flowing channels, which would be prone to erosion.

You will likely want some check-dams in the main waterway itself was well. You want to raise and slow the water level, so that the percolation back to your channels is more gentle, and has a bit more depth.

What are you planning to plant? Sounds like a fun project. I wonder what the EPA will say about it though.

I think more important than angle to the creek is deeper than the creek/dam or sloping upward to drain out as the water level drops.  If you want it to hold water longer like a Chnampas then deeper. It is something you can experiment with by digging some deeper than others and adjusting to what works best.  
The plan sounds good to deep hydration further from the creek and keep the root zone above the winter waterlogging.