Remove the stopper from the carboy. Place the funnel into the bottle opening. Fill the bottom of the bottle with a layer of potting soil 2 inches deep.
Cover the potting soil with a 1/2-inch layer of builder's sand. Make the sand layer as even as possible, making sure you completely cover all the potting soil.
Place a yardstick into the opening of the bottle. Set the bottom end of the yardstick on the sand bottom, right up against the wall of the carboy. Let the top end of the yardstick lean on the bottle opening lip. Gently trickle water down the yardstick by pouring it, in small amounts, from a cup. This will start to add water to your ecosystem without disturbing the layers of potting soil and sand.
Continue filling the bottle with water, switching to pouring it without the yardstick when the water is deep enough that you won't disturb the bottom surface. Leave a 2-inch space at the top of the bottle for an air pocket. Leave the bottle out, without the top, for at least 48 hours. This will allow any chlorine in the water to be released into the atmosphere.
Push three pieces of aquatic plant matter into the bottom of the soil by threading them onto the tines of a barbecue fork. Shove the plant down into the soil, then gently loosen the fork from the leaf, leaving the plant in place. Use a common aquatic plant like Anacharis, Vallisneria or Elodea.
Add three snails and two guppies to the water. Float two or three pieces of duckweed in the water.
Place the plug back into the opening of the bottle. Seal the bottle completely by covering the entire top with layers of duct tape.
Place your aquatic ecosystem in a place that it gets indirect sunlight.