Seagrasses - the underwater plants that act as nursery grounds for young fish - need more protection, say scientists.
Monitoring of seagrass meadows off the North Wales coast found areas damaged by the likes of boat moorings, anchors and vehicles crossing at low tide had reduced value to the ecosystem.
Fewer species of fish were found where seagrass was degraded, according to research published in PeerJ journal.
The seagrass studied was near the village of Porthdinllaen, in Gwynedd.
Researchers at Swansea University studied areas with both high and low cover over a 28-hectare stretch of sea bed.
They also sampled fish living in the underwater meadows of flowering plants.
There was a three-fold reduction in the diversity of fish species and invertebrates, such as prawns, shrimp, juvenile cod and juvenile plaice, in areas of low cover, said lead researcher Dr Richard Unsworth.
He said that in the areas that had become damaged, there was "a reduction in diversity of the species and in the value of the habitat for juvenile fish".
The seagrass is in a special area of conservation, which is a strictly protected site under the European Habitats Directive.
However, despite this protection it was still being degraded, he said.
"We have a lot of legislation in the UK already to conserve a lot of marine habitats but these mechanisms do not have enough financial clout," said Dr Unsworth.
Dr Jean-Luc Solandt of the Marine Conservation Society said the study reaffirmed that seagrass meadows are important habitats that should be protected.
"This research shows that disturbance to seagrass beds negatively impacts on ecosystems, and the capacity for these habitats to support a wealth of species.
"It is further evidence that protection measures are needed to preserve these diverse but fragile places."
Seagrasses are also found in several marine conservation zones off England.
Some marine conservation zones have already designated, with others due for consideration next year.
Conservation groups, backed by MPs, have been calling for a full network of protected zones to be created around the coastline of the UK.
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