How to build chinampas on a pond without getting stagnant water problems

I've often though about putting in a pond with finger like chinampas extending into the water. However, wouldn't the water between the fingers go stagnant and cause problems with algae growth? How could this be prevented?

Gilbert, I'm wondering if you had just short of a full step's space every few feet down the length of the chinampa, while keeping the smaller chinampas connected below the surface, you could maintain decent water circulation.

NOT speaking from experience, just pontificating. If possible, place the chinampas on the upwind side of your prevailing summer winds. That way any scum and algae forming in those pockets will be blown out to the middle of the pond. I usually see one spot on a pond where the algae tends to collect, don't put chinampas there. If algae is a problem, grab a rake, scoop it out, and place directly on the chinampa. Instant fertilizer! Again, not from experience, but I have been thinking of this same idea, just haven't put into practice yet.