Algae are weeds in the water garden container. They can be controlled through natural means and through chemicals. Algae need water, sunlight, and nutrients to grow. We can't take away the water, but we can limit the sunlight and nutrient levels. Shade can be created by locating the pot where it doesn't get too much sun and by planting lots of plants in the water garden. Excessive nutrient levels in small containers tend to come from the fertilizer tablets placed in the soil of the plant pots. Make sure such tablets are completely covered with soil.
Underwater plants and floating plants get their nutrients directly from the water and compete directly with algae for nutrients. Floating plants shade the water, too. Potted plants get the majority of their nutrients from the soil in the pots and only compete for sunlight.
There are a few algicides that are safe for other aquatic plants, fish, and the other organisms found in backyard ponds and water garden containers. Algaefix from Aquarium Pharmaceuticals was the first of these products and can be used in aquariums as well.