Salt concentration should be first environmental filter. Most groups are sensitive to salt concentration which tends to vary temporally and spatially in these systems. 

Water quality, temperature and pH will also be key factors to consider.

Phytoplankton community as the ist trophic level of the food chain..

Most important factor for macrobenthic assemblage in coastal lagoon especially transitional water is salinity and another factor or second factor in my opinion is substrate type.

Regards

I agree, under normal conditions salinity is the controling factor, followed by sediment grain size.  Not knowing the location of Chilika Lake, I looked it up on google earth and my first thought was that it looked similar to the coastal estuaries along the U.S Gulf Coast (Louisiana, Mississippi, Alabama, Georgia).  Then I noticed the apparent cloudy nature of the water suface.  If that represents sediment entering the lake then that is a significant sediment load.  In that case I think sediment grain size is probably the controllong the community of the lake.

Wave action, tidal amplitude and salinity. Sediment texture also is a regulating agent.

Thanking you all for your kind reply.

Generally, The community structure of benthic macroinvertebrates

can be influenced by sediment particle size (Van Hoey

2004), salinity (Pinder et al. 2005), availability of food and

nutrients (Frost et al. 2009), anthropogenic pollution and

pH (Goto and Wallace 2010).

I studied benthic community of one costal lagoon in Egypt. I believe that the major variable is salinity, water current and bottom nature respectively. one more factor is the area of the lagoon and the effect becomes obvious near its opening to the sea.

Dear Montaser Hassan ,

Would u like to explain in detail regarding the role of lagoonal opening to the sea in relation to the macrobenthos community of the coastal lagoon

Pollutants are the major impact on benthic community. Industrial and sewage pollution disturb the soil, soil become loosen and anaerobic, ultimately the macro benthic animals gastropods and bivalves and other biological  organisms lose their substratum, so survival is very difficult. If we provide artificial substratum such stones or concrete reefs, they can attach and grow more.

This is study conduct on the mollusk community of a lagoon which presents two different openings to the sea .The community is mostly affected by salinity, temperature and organic content of the sediments

Article The evolution of the molluscan biota of Sabaudia Lake: A mat...

There are different geographical factors that can affect this answer. Lagoons in coastal areas are situated in different physical and chemical environments. For example lagoons situated in coastal areas with large freshwater discharges would most certainly be affected by the single factor of large swings in salinity while those within strict polyhaline conditions with little variation would be affected by other factors such as sediment and organic matter or as someone suggested Pollution from sewage and other  large scale human discharges. 

I think deoxygenation of sediments is a major factor, whether caused by organic sediments or pollution. Also, if there are periodic saltwater intrusions, they may lie under less saline layers and not mix with them, separated by a halocline. The denser saline layer will become deoxygenated by decay of algae etc. and while some mobile benthic members such as crabs can visit and scavenge for short periods, they cannot live there.

Physical factors affect the zonation of macrobenthic community in the intertidal domain

in lagoon environment  sedimentation is prime factor for distribution macrobenthic community and associate flora like sea grass sea weed have a prime role to attract the marobenthic community