Dozens of the 127 proposed marine conservation zones, including one on the Isle of Wight, were judged by Government advisers to be at high risk but wildlife groups were left dismayed when it emerged they would not be immediately protected.
One such site is Bembridge, a coastal area to the east of the Isle of Wight, which is made up of a mosaic of habitats from limestone reefs to sand and gravel beds.
It is home to a number of important species and habitats which the marine conservation zones are focused on protecting, including maerl and peacock's tail seaweed, kaleidoscope stalked jellyfish, short and long snouted seahorses and seagrass beds.
Sea bream breed in the thin layer of gravel in the bay, while the rocky areas are habitat for sponges and juvenile edible crabs, which can be seen scuttling for cover when rocks are upturned.
Unlike some proposed sites, Bembridge has been well studied, enabling conservationists to provide plenty of evidence of the species which are there, according to Jolyon Chesworth, head of marine conservation for Hampshire and Isle of Wight Wildlife Trust.
"Bembridge is well known, it's been well researched and there's lots of evidence going back 40 to 50 years, so we've got a good idea not just of what is here but what was here. It's a really quite complex matrix of habitats in this area that makes Bembridge particularly special," Mr Chesworth said.
It is a key site for rare species, such as the once- common peacock's tail seaweed, now only found off the shores of three counties, with the Isle of Wight the national stronghold and Bembridge the stronghold across the island.
Mr Chesworth said the area was not at risk from the most damaging of activities such as dredging, but there were issues with some kinds of fishing and anchoring of ships, including commercial vessels heading for Southampton Port. "If they weren't managed, these habitats would be at risk," he warned.
In its decision on whether to designate Bembridge, the Environment Department (Defra) said that while there was evidence it was important for a number of species, costs would top £183,000 a year, mostly as a result of impacts on recreational sailing. There would also be "significant unquantified cost" associated with cargo ships anchoring outside Southampton Port, which needed further assessment.
But Mr Chesworth said officials had not taken into account the potential benefits of designation, including boosting small-scale fisheries such as crab potting which would be allowed to continue. He said the evidence required for environmental assessment was greater than for socio-economic impacts.