Some gharials may be feeding on fish that have large toxic loads
Measuring up to 6m long, with elongated narrow snouts, gharials are one of the world's most distinctive-looking crocodilians.
Just 100 years ago, these fish-eating reptiles were prevalent throughout the Indian subcontinent; but by 2007, there were just 200 breeding adults found in only a handful of rivers in India and Nepal.
Last winter, this already critically endangered species was dealt another cruel blow. Over the space of just five months, more than 100 of the creatures washed up dead on the banks of India's Chambal river - and nobody knew why.
For the past year, herpetologist Rom Whitaker, who runs the Madras Crocodile Bank, has been followed by a BBC Natural World team as he attempted to solve this mystery.
Here, he explains how scientists may finally be on the verge of finding some answers.
Autopsies suggested that gout was responsible for the gharials' deaths
It's been a bit like a long drawn out Agatha Christie mystery. Everything we hear about just throws up more questions.
Why is it just a particular 40km stretch of the river that is being affected, and the deaths all occurred over winter?
Why is it that only one particular size class - the medium sized ones - is dying?
And why is it that only one fish-eating animal is being affected?
Death by gout
We started to speculate that it had to be something in the food chain.
Autopsies have told us the deaths were caused by gout, which more or less indicates kidney failure - and this points to the build up of toxins.
The river that they live in - the Chambal - is one of the cleanest rivers in India. But this flows into another river called the Yamuna, which is a big huge toxic mess.
We think the gharial are moving into the Yamuna and feeding on fish that have big toxic loads.
Then it is likely that they are coming back to the Chambal, having brought with them all this fish they have gorged upon, and this bioaccumulation of toxin is then affecting them.
We believe that the die-off happened in winter because when it is cold, the animals are unable to metabolise anything in their system - they sort of shut down.
This will take a toll on weak, injured or sick animals. And in this case, if they had damaged kidneys, and the kidneys were trying to excrete the uric acid but were unable to, then the uric acid would have spread to the body, causing gout.
Could sights like the mass-hatching of 500 baby gharials soon be a thing of the past?
Ecologist Jeff Lang was able to fill us in on another piece of the puzzle concerning the size of the animals that were dying.
The little crocodilians can bask in what little sunshine is available in the winter, and because they are small they heat up very fast. Even if they have eaten polluted fish, they would be able to metabolise it very fast - in other words, get rid of it as quickly as they consume it.
The pieces of the puzzle are beginning to all come together
The very large animals are at a stage of their life where they are not gorging on fish as they have no great incentive to grow fast. They are more likely to be concentrating on patrolling their territory than on feeding.
It is the medium-sized class that are dying - these are feeding on a lot of fish as they want to grow quickly. And in the case of the adult females, they need extra energy for egg production at this time of the year.
But being larger, it takes them a heck of a long time to warm up, and we think that they never do warm up enough to aid digestion and metabolise out the toxins.
But why aren't other fish-eating animals affected?
If you are talking about river dolphins, cormorants, otters and pelicans - these are all warm-blooded, and they are eating and expelling waste as fast as they can.
So this accumulation may take place, but it isn't happening fast enough to kill them - at least not yet. And of course, there is the sinister possibility that people who eat the fish may also be affected.
The other species of crocodile that's there is the mugger crocodile.
And this animal is not a specialist like the gharial.
Gharials only eat fish, but these muggers eat anything that moves. So we surmise they are not getting the same kind of accumulation of nasty fish in their systems.
This is all speculation - but it is educated speculation. The pieces of the puzzle are beginning to all come together. But it is not enough to just find out what happened.
Could gharials be the canary in the coalmine for India's rivers?
If they are going to clean up the Yamuna river, we are talking probably about another long decade of really hard work - and there is a chance that a die off could happen again before that.
The Chambal population is the most important last repository of gharial. So it seems that a critically endangered species with this one last bastion left is in real real trouble.
But the problem goes much wider.
The gharial could be the canary in the coalmine. They are telling us something very important - that our rivers are dying, and that could mean us dying next.
Crocodile Blues is on BBC2 on Tuesday 2 December at 2000GMT as part of the Natural World strand
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