Because you have a few of the ingredients needed for an active atmosphere, a sun that provides heat, air that provides a medium through wich heat and water can travel, a variable landscape which gives temperature and air pressure variance, you get wind, thorugh maybe not reguar, north-east-west-south wind, condensation, varying temperature, clouds, rain, e.t.c.
Though hail, snow and extremely cold weather would be more or less out of the question, with rain storms being an exception, because I think being that deeply rooted in a planet\'s crust would mean closer to its core, and thus tropical weather year-round.
wind would probably occour blowing into and out of the stagmilite, or a spiral motion due to the step-ladder geography of the stagmalite.
Rain could occour for a few reasons, evaporation of the water in the great lake, the rivers of the different levels, and perhaps the water that seeps into the stagmilite near the crystal would instantly be vaporized at that proximity.
*edit: fog would be a natural occourance with the conditions I described above which would build up in the lower levels and \"fill\" the stagmalite. This great amount of fog could account for sufficient blockage of the sun\'s rays and perhaps dramatic temperature variences. Making the stagamalite perhaps a reverse mouintain in terms of climate....well, at least seasonally.
