Birds such as the puffin could be affected by a decline in zooplankton
Experts on invertebrates have expressed "profound shock" over a government report showing a decline in zooplankton of more than 70% since the 1960s.
The tiny animals are an important food for fish, mammals and crustaceans.
Figures contained in the Department for Environment Food and Rural Affairs (Defra) document, Marine Programme Plan, suggested a fall in abundance.
Charity Buglife said it could be a "biodiversity disaster of enormous proportions".
They said it could have implications for creatures all the way up the food chain, from sand eels to the seabirds, such as puffin, which feed on the fish.
Defra described the Marine Programme Plan as one of the department's high impact programmes, reporting directly to the Defra board and used to guide policy.
Buglife director Matt Shardlow has written to Rodney Anderson, director of marine and fisheries at Defra, praising the level of information in the document but also expressing the organisation's serious concerns.
In his letter, seen by the BBC Scotland news website, Mr Shardlow said: "The disappearance of butterflies, moth, bees, riverflies and other small animals is an environmental tragedy.
"But, despite this experience, we were profoundly shocked to read that zooplankton abundance has declined by about 73% since 1960 and about 50% since 1990.
"This is a biodiversity disaster of enormous proportions."
A graph shown in the report charts a steady decline in zooplankton from 1990 to 2006.
Buglife Scottish officer, Craig Macadam, said climate change could be a factor.
He said: "Zooplankton is the basis of many food chains in the marine environment.
"Without them it is going to cause problems further up the chain."