Detritus and nutrient dynamics in mangrove ecosystems and man-made freshwater wetlands, phytoremediation potential of wetland plants, ecological engineering techniques for waste water treatment using wetlands and wetland plants, indigenous knowledge on aquatic resource conservation and management, decision-support systems for natural resource management, mangrove and sea grass ecology

• Perera K.A.R.S. and Amarasinghe M.D. 2014. Effect of vegetation structure on carbon assimilation capacity of mangrove ecosystems in the east coast of Sri Lanka. J. Coast. Dev. 17:382. doi: 10.4303/1410-5217.1000382
•  Perera, K.A.R.S  Amarasinghe, M.D. and Somaratna, S. 2013. Vegetation structure and species distribution of mangroves along a soil salinity gradient in a micro tidal estuary on the North-western coast of Sri Lanka. American Journal of Marine Science 1 : 7-15. doi: 10.12691/marine-1-1-2.
• Madurapperuma, B.D., Amarasinghe, M.D. and Oduor, P.G. 2013. Salient ecological functions of a tropical freshwater wetland. Lakes & Reservoirs: Research & Management 18: 45–51. doi: 10.1111/lre.12019
• Amarasinghe, M.D. and Pugh Thomas, M. 1995. The environmental impact assessment system in Sri Lanka, with special reference to the shrimp farming industry. The International Journal of Environmental Education and Information, 14(3)
• Amarasinghe, M.D. and Balasubramaniam, S. 1992. Structural properties of mangrove stands on the north western coast of Sri Lanka. Hydrobiologia , 247: 17-27
• Amarasinghe, M.D. and Balasubramaniam, S. 1992. Net primary productivity of two mangrove forest stands on the north western coast of Sri Lanka. Hydrobiologia, 247: 37-47
• Amarasinghe, M.D. 1997. Ecological functions of mangrove and related ecosystems and their contribution to economic sustainability. Sri Lanka Journal of Aquatic Sciences, 2: 1-20
• Amarasinghe, M.D. 1997. Leaf litter decomposition in the mangrove ecosystems of Dutch bay, Sri Lanka. Sri Lanka Journal of Aquatic Sciences, 2: 21-28
• Pahalawattaarachchi, V. and Amarasinghe, M.D. 1997.Leaf litter decomposition and changes in leaf C:N ratio in the mangals of Negombo lagoon (Sri Lanka). Sri Lanka Journal of Aquatic Sciences, 2: 29-42
• Amarasinghe, U.S.; Amarasinghe M.D. & Nissanka, C. 2002. Investigation on the Negombo estuary (Sri Lanka) brush park fishery with an emphasis on community based management. Fisheries Management and Ecology 9: 41-56
• Amarasinghe, M.D. & Jayamanne, S.C. 2004. Functional evaluation for wetland management: A case study from a river basin in Sri Lanka. In J.M. Jahi, K. Arifin, S. Surif & S. Idrus (eds) Proceedings of Second World Conference on Environmental Management, Universiti Kebangsaan Malaysia: 65-71
• Amarasinghe, M.D., Liyanage, J.A & Nirbadha, K.G.S. 2004 Presence of heavy metals in lants of a tropical freshwater wetland in Sri Lanka as an indicator of their relative phytoremediation potential for heavy metal contaminated water from urban runoff. In J.M. Jahi, K. Arifin, S. Surif & S. Idrus (eds) Proceedings of Second World Conference on Environmental Management, Universiti Kebangsaan Malaysia: 311-319

Phytoremediation potential of freshwater wetland plants, plant-based wastewater treatment systems, diversity and distribution of mangroves and sea grasses, coastal resources management.

• Plant ecology, tropical wetland ecology and management, EIA and environmental assessment, environmental management, production of audio-visual teaching material, interpretation of remotely sensed data and preparation of maps