I was little confused by the 4 second timer - it sometimes let me keep playing when the time ran out, and sometimes didn’t, and I couldn’t figure out why

This is good feedback. What happens when the timer runs out is that you lose a heart in your health bar at the top, which is not great because it’s not very prominent, so it’s difficult to see it happen as a cause and effect. The intention was to provide a way to replenish that health during the second phase of the game, where you have to navigate in the water for an extended time.

I think if I was to do it over again, I’d get rid of the other health damaging effects (the spikes) and just have a longer timer, and then have something akin to the air bubbles in sonic the hedgehog to replenish your breath for the longer underwater segment.

Yes! Very intentional!

I think the level design could use some work to make it more interesting to figure out how to work with the water to navigate the level.