Even before I was a travel writer, I approached sights described as "magical" with a good deal of skepticism. Too often, I have been promised miracles and delivered slights-of-hand – the usual bravura and bluff of tourism. The bioluminescent bay in Vieques, Puerto Rico was one of the few places that made good on its promises. Maybe the only one. By day, the warm shallow bay looked unremarkable, even somewhat dingy compared to the crystalline waters of nearby Caribbean beaches. But at night, the flash and spark of the tiny phytoplankton in this Mangrove lagoon filled me with literal awe. It was like living lightning.

Since January, however, the bay has gone dark – and no one knows why.

Theories abound, as a number of articles have explored in the last few months: too much human usage, or strong winds that have disturbed the bay's infinitesimal inhabitants. Like many rare ecosystems, bioluminescent bays are fragile, and the shifting patterns of both weather and tourism can affect them greatly. But it's been hard not to notice what's been missing from these discussions: climate change.

This oversight is particularly glaring given that this isn't the first of Puerto Rico's bioluminescent bays to go dark in the last year. Grand Lagoon – just a ferry ride away from Vieques in the town of Fajardo – went out for most of last November. The same explanations were debated then: unprecedented extreme weather events, or run-off from several nearby construction sites. No doubt either – or both – were contributing factors. But somehow, the conversation (at least in the media) never seemed to connect what was happening in Fajardo with global environmental concerns.

Given the ever-increasingly serious warnings about climate change – which 97% of climate scientists now agree is caused by human activity – it would seem to merit at least a small place in the popular discussion of these back-to-back mysterious ecological collapses.

Scientists who specialize in bioluminescent plankton have – to little fanfare – already warned us that these creatures are endangered. Two years ago, Dr Michael Latz, a researcher at the Scripps Institution of Oceanography, told New Scientist magazine that "as global warming changes ocean flows, these micro-organisms are increasingly at risk". Scientists at Canada's Dalhousie University showed that, since 1950, the worldwide population of phytoplankton has declined by 40% due to the rising sea surface temperatures caused by a warming planet.

We also know that the indirect effects of climate change have dangerous ramifications – the likes of which we are only just beginning to comprehend. Those strong winds and extreme weather events that have buffeted the bays? Increased sea surface temperatures – driven by climate change – may contribute to them as well, as we know from studying hurricanes. "The intensity, frequency, and duration of North Atlantic hurricanes ... have all increased since the early 1980s" reports the 2014 Third National Climate Assessment: "The recent increases in activity are linked, in part, to higher sea surface temperatures."

Like a pot being brought to boil, the seas are heating up.

The first time I visited Vieques in 2006, tour operators encouraged me to swim and kayak in the bay, but told me to avoid the motorboats, since their dirty engines created diesel-fuel dead zones. Since then, locals have developed new conservation guidelines: no swimming or touching the water with your skin at all – things I wish I had known not to do. But these and other protections have done nothing to save the bay's famed bioluminescent organisms.

But this isn't just about one or two tourist attractions on small islands in the Caribbean. Bioluminescent bays are rare because they are much more fragile than your average marine ecosystem. Like canaries in the proverbial coal mine, their loss is a warning that hardier creatures and more common shores will be endangered soon.

I was taught in elementary school that we live in a world with five oceans – an idea that feels laughable now. There is only one ocean – the world ocean, a vastness that ignores the political demarcations of maps and men. Its problems cannot be solved piecemeal, and more and more studies suggest that we might not "solve" them at all. Long before we detonated the first nuclear bomb or undertook a Cold War, nature invented the idea of mutually assured destruction – and she might just hold true to her end of the bargain.

If we are to do anything to begin to address the problem we have created, it will require a clear-eyed look at its true magnitude, and an understanding of the interconnectedness of our world – and its waters. Environmental concerns must be integrated into personal, political and commercial decisions on every level. We can no longer pretend that our trash disappears forever when it hits the wastebasket, or that we are not implicated in the environmental degradation of the far-away countries who now supply our ravenous need for consumer goods.

The phrase "think globally, act locally" might be mocked for its utopianism, but it's a mantra we need to heed when it comes to the environment. Otherwise the lights will continue to go out, in Vieques and around the world.

I don't even have a good picture of the Vieques bio bay to remember it by – like all real magic, it looks shoddy in reproduction. Perhaps, like the Grand Lagoon, it will come back, at least this time. But how often must nature flip the switch before we start paying attention?