Heathrow risks breaching European Union air quality regulations by 2010 because of poor ground traffic access links, they said.
London First, which represents the capital's leading employers, supported expansion at Heathrow, but said environmental concerns need to be addressed first.
The London Assembly opposes plans for a third runway.
It said the expansion plans had exaggerated economic benefits and that carbon trading costs have not being adequately factored in.
More should be done to encourage people off short haul flights and onto rail, said the Campaign for Better Transport.
The green lobby group's response to the consultation claims 45% of all flights within Europe are for distances of 500km or less. It said more high speed rail links should be created north of London, with rail links from Heathrow to the rest of the country also needing improvement.
The Society of British Aerospace companies (SBAC), which backs the third runway believes an expanded Heathrow can be achieved within the existing noise limits, because of the introduction of quieter, greener aircraft.
Heathrow is the busiest international airport in the world, and currently handles 478,000 flights per year.
Expansion plans could send this figure up to more than 700,000 by 2030, an increase comparable to Gatwick's existing capacity.