Finding fish in murky waters: TropWATER study guides best monitoring methods in seagrass meadows

Murky waters, resident crocodiles, dense seagrass, and elusive species make studying fish in seagrass meadows challenging – testing the limits of available monitoring techniques.

A new study by James Cook University TropWATER scientists explores the benefits and limitations of monitoring techniques for fish and prawns, providing a practical roadmap to help researchers choose the right tools for the right conditions in seagrass habitats.

The team reviewed 13 common methods, from nets and trawls to underwater cameras, sonar, and cutting-edge environmental DNA (eDNA). Each method has trade-offs. Some risk disturbing seagrass, others falter in turbid water, while eDNA excels at detecting species but cannot yet measure abundance.

Darcy Philpott, a PhD student with TropWATER and lead author of the study, said the research provides an important guide for choosing the right monitoring techniques.

“Studying fish and prawns in seagrass meadows is challenging, with species behaviour and traits making them hard to find,” she said.

“Our message is that no single method gives you the full story. By combining complementary techniques, researchers can capture a more complete picture of biodiversity without disturbing these habitats.”

The research was supported by the partnership between North Queensland Bulk Ports Corporation and James Cook University through a scholarship and research funding. JCU TropWATER conducts annual seagrass monitoring as part of this partnership, collecting over 30 years of data in ports.

Professor Michael Rasheed, seagrass scientist and program lead, said without reliable monitoring, declines in these habitats could go unnoticed until it’s too late.

“We can’t protect what we can’t measure. Better monitoring tools mean better management and stronger conservation of seagrass meadows and the fisheries they support,” he said.

“We have a strong commitment to work with industries to ensure the habitats surrounding Ports are well protected and managed in a way that has minimal impact on the local environment.

“This NQBP partnership has allowed us to take this monitoring further – we can assess what we do, improving our techniques and sharing this knowledge with other researchers and with port managers.”

Future work will focus on refining monitoring approaches to improve biodiversity assessments while reducing environmental impacts.

The study is published in Marine Environmental Research: https://doi.org/10.1016/j.marenvres.2025.107395