Why does my aquatic eco system smell like sulfur?

The sulfuric smell your experiencing is completely normal. The containment of waste along with the plant life's cycle could be a mixture of the smell being created. Along with those elements the iron balance along with several other sources such as ph levels could be other sources contributing to the smell. Since your dealing with fresh water this is all very normal. If you were dealing with a pool the answer would be to add chlorine to cancel out the smell, but since this isn't the case and you dealing with living beings just leave it as it. They are fine ;)