Action will be taken against the illegal removal of trees.
The protected marine areas are the Kandi-Hera Maakandu channel and the British Loyalty shipwreck.
The Chinese company said there was a detailed seabed cleaning plan.
Photos show shark fins hung out to dry by Sinamalé bridge workers.
The ministry uprooted trees and carried out road construction without an environmental impact assessment.
The fines were imposed over the unauthorised extraction and release of groundwater.
The three biodiversity hotspots include popular dive sites and unique wetlands.
Hoadehdhoo islanders dug out the causeway after swell surges flooded the island.
The fish was said to be tasty but with very thick skin.
Raalhugandu was fenced off in 2016 for the construction of a bridge.
Nearly 70 percent of the mangrove has been reclaimed, NGOs said.
The government wants to do a test landing before a presidential election on September 23.
Developing an airport on Kulhudhuffushi was a campaign pledge of President Abdulla Yameen.
The death toll from floods in Kerala state rose to 79 by Thursday afternoon, the Times of India reported.
Details of the damage have been shared with resorts and the National Disaster Management Centre.
Neither the Housing Ministry nor the island council has contacted families about relocation plans.
An airport and hotel project would swallow up most of Fainu island.