Filters will stop sediment from clogging lines but algae can grow after the filter and be a big nuisance. The combination of warm water, light, and nutrients are the best recipe for fast algae growth. Prevent as much light as possible from getting into your reservoir and supply lines.

You can also use chlorine or hydrogen peroxide to stop or kill algae already growing. In most systems, the hydrogen peroxide will dissipate before it gets to your plants.