The noisiest planes will face a trebling in charges to £9,000 per landing, although fewer than 1% of flights fall into this category.
The airport hopes the move will provide more incentive for airlines to fly cleaner and quieter planes.
Some fares should fall as Heathrow is proposing to give a £10 discount to the average £29.59 per passenger charge for domestic flights, although the charges are levied on airlines rather than customers so are not necessarily passed on.