I would think a stream of rocks connecting the two bodies will eventually get old, as it continues to be problematic. Maybe I'm projecting, as it is everything I can do just to brush my pool once in a while. Emptying a stream of rocks a few times a year to scrub everything down, and fight with chemistry in between? I wouldn't last a month.
Is there a water fall at both ends, or just at the bottom?
Some ideas, mix'n'match, or a la carte:
Plumb the spa directly to the pool with a PVC pipe. (This is the foundation of the following ideas.)
Optionally, maintain the water fall at the bottom.
Turn the stream into landscaping (hide the pipe connecting the spa/pool in the landscaping). Use dirt and some boulders. Plant "stream-like" foliage.
Turn the stream into landscaping. Use less dirt, but enough to plant plants, and use more rocks, various sizes (what you already have).
Turn the stream into landscaping. Use all rocks, and plant plants outside of the stream. A dry creek.
Use all blue rocks and/or glass, of different hues, and simulate a stream. (See pic below.)
Is the stream level enough to hold water? Turn it into an independent water feature, as a separate body of water, with it's own pump and filter (small AG rig). You could create/recreate waterfall at top of stream. No plants.
Or independent water feature with water plants. It'd be a pond at that point. You'd still have to maintain this separate body of water, but not too carefully, and it wouldn't affect the pool.
If not level enough, install a serious of large bowls, or concrete partitions, and let the water spill from each into the one below, top to bottom. Maybe add some shoots if it's too many bowls to fill the stream with just bowls. Small pump would send water from the bottom bowl back to top. Bottom bowl would need to be large enough to hold all the spilled over water when not running (but not necessarily all the water of every bowl, as most of that would stay in each bowl). Plumb in a water filling system, to offset evaporation (I have drip tubing running from hose bib to fountain). Surround bowls with rocks and plants.
Convert it to a water slide, but spa would still be connected independently to pool. Water for slide would pump from the pool. Nothing in the slide, so it'd run clean with pool water, or be dry when not in use.
That's off the top of my head... Others will no doubt chime in with other ideas...
