There are several steps to reduce algae in aquaponic systems. First, cover any exposed water; we use shade cloth that is either made to fit the tank or hung above the fish system. Also, minimize the amount of time that your raft boards are removed from your DWC to reduce light exposure. Next, add another species of fish or invertebrate that eats algae. Plecos are a great species to co-habitat in your fish tank to eat large algae and detritus.
Outside of the shade cloth, the use of seaweed extracts, or humic substances can darken the water and naturally reduce algae growth. They also have growth and immunostimulatory effects on the plants, helping them become more resistant to disease and pest. A couple of products we sell for this are MaxiCrop Soluble SeaweedCytoPlus, and Espartan.
While you do not want overly abundant populations, you will always have some amount of algae throughout the system. Do not be too concerned with micro-algae. There are numerous accounts of beneficial interactions between plants and micro-algae, which suggests that the algae may store carbon for later use by microbes and either directly or indirectly for plants resulting in increased growth. Your fish will also benefit from it!