Begin by brushing brown acrylic paint from the center of the pond outward to about an inch of the shoreline. Dip your brush in water to dilute the color a bit nearest the shore. After the brown has dried put a small amount of black paint in the area you want the water to look the deepest. Dip your brush in water and blend the edges of the black into the brown. Let dry completely.
Envirotex is a two part epoxy-like coating used for craft projects. This is the best way of making realistic water that I've found. It is available from us or craft and hobby stores. Mix equal parts in a clean cup and pour it into the pond. It will level itself but you can help it out with a small brush if you like. It takes overnight to dry.