For water you can use a waterprocessor or a water filter.
Both can be added via Code and the second one should be supported by the sdks scene Composer.
So you have to be clear what you are looking dir or which Tutorials you refer to (out Wiki?)
SimpleWaterProcessor waterProcessor = new SimpleWaterProcessor(assetManager);
waterProcessor.setReflectionScene(rootNode);
// we set the water plane
Vector3f waterLocation = new Vector3f(0, -58, 0);
waterProcessor.setPlane(new Plane(Vector3f.UNIT_Y, waterLocation.dot(Vector3f.UNIT_Y)));
viewPort.addProcessor(waterProcessor);
// we set wave properties
waterProcessor.setWaterDepth(50); // transparency of water
waterProcessor.setDistortionScale(0.05f); // strength of waves
waterProcessor.setWaveSpeed(0.05f); // speed of waves
// we define the wave size by setting the size of the texture coordinates
Quad quad = new Quad(1000, 1000);
quad.scaleTextureCoordinates(new Vector2f(10f, 10f));
// we create the water geometry from the quad
Geometry water = new Geometry("water", quad);
water.setLocalRotation(new Quaternion().fromAngleAxis(-FastMath.HALF_PI, Vector3f.UNIT_X));
water.setLocalTranslation(-500, -58, 500);
water.setShadowMode(ShadowMode.Receive);
water.setMaterial(waterProcessor.getMaterial());
rootNode.attachChild(water);
Create a scene node, attach your terrain/Geometry and sky to the node, then add scene node to your rootNode. Attach water and light to rootNode. Use the scene node for reflection.
waterProcessor.setReflectionScene(scene);
Edit, forgot to say why,
public void setReflectionScene(com.jme3.scene.Spatial spat)
Sets the reflected scene, should not include the water quad! Set before adding processor.