Freshwater crocodiles might start popping up in places they have not before, after an annual survey of crocs in a Western Australian gorge recorded its lowest numbers in five years.

Researchers have monitored freshwater crocodiles at Windjana Gorge in the West Kimberley since 2014, as part of a research project to monitor the population's health ahead of the inevitable arrival of cane toads to the area.

While as many as 260 crocs were spotted in the gorge during the 2016 spotlighting survey, just 45 were spotted this year.

Up to 80 crocodiles have been caught, measured and weighed during previous surveys, but this year researchers only managed to catch 19.

Rangers at Windjana Gorge during the recent survey of freshwater crocodile numbers. ( Supplied: Parks and Wildlife Kimberley/Max Jackson )

Department of Biodiversity, Conservation and Attractions conservation coordinator Tracy Sonneman said this year's survey had recorded the lowest numbers since the program started.

Ms Sonneman believed this was due to last year's wet season in the West Kimberley, which was one of the biggest on record.

"With the last two really good wet seasons we've had, I think they are just dispersing through the landscape," she said.

Ms Sonneman said it was unclear where the crocodiles would have moved to, but they might be found in new areas.

Windjana Gorge is a popular site for tourists, and normally home to many freshwater crocodiles. ( ABC Kimberley: Emily Jane Smith )

"They might be in areas that you haven't seen them before. There may even be water in areas that you haven't previously seen," she said.

"Windjana is a reliable location for them and they often use that. But with the good wets we've had you may be seeing pools in areas where you wouldn't see them.

"Or you may be seeing higher numbers of the freshwater crocs. We don't know where they have gone entirely."

Ms Sonneman said during previous surveys the researchers had re-captured a crocodile that had travelled more than 20 kilometres during the wet season.

Researchers also traversed the caves of nearby Tunnel Creek in their bid to survey crocodile numbers. ( Supplied: Parks and Wildlife Kimberley/Lachlan Gilding )

As well as recording fewer crocodiles, the researchers also found lower numbers of barramundi, freshwater turtles and sawfish in the gorge.

"Again, I think it is just that dispersal throughout the landscape with the really good wet seasons," Ms Sonneman said.

The survey results play an important role in measuring the impact cane toads may have on the crocodile population.

A freshwater crocodile relaxes on a bank at Windjana Gorge. ( ABC Kimberley: Lisa Herbert )

The pests have crossed the border into the eastern Kimberley and are expected to reach Windjana Gorge within the next three years.

Ms Sonneman said cane toads travelled about 50 to 70 kilometres a year and had most recently been recorded about 200 kilometres away from the gorge.

"Without having this long-term dataset we may blame some of the things that we see on toads unfairly," she said.

"So this gives us that seasonality of the natural changes that would occur in the system compared to the impact that the toads might have."