The Atlantic menhaden population is subject to a high natural mortality rate. There is a somewhat reduced probability of death from natural causes when the population is being harvested. Natural mortality is also higher during the first two years of life than during subsequent years. Scientific studies indicate an annual instantaneous natural mortality rate (M) of 0.45 in the absence of fishing; this rate is equivalent to an annual reduction in population numbers of 36%. This rate is quite high compared to other pelagic marine species. Atlantic herring, for example, is characterized by an 18% annual natural mortality rate. During the 1955-1987 period, under exploitation, the annual natural mortality rate for age-1 Atlantic menhaden was 30% and, for ages 2 and older, it was 20%. Natural mortality removes an estimated 30% of the exploited population at age 1 and 20% each year thereafter.

Menhaden natural mortality is probably due primarily to predation, since the fish are so abundant in coastal waters during the warmer months of the year. All large piscivorous sea mammals, birds, and fish are potential predators on Atlantic menhaden. Menhaden are preyed upon by species such as bluefish, striped bass, king mackerel, spanish mackerel, pollock, cod, weakfish, silver hake, tunas, swordfish, bonito, tarpon, and a variety of sharks .

Coastal pollution and habitat degradation threaten marine fish species, such as Atlantic menhaden, which spend their first year of life in estuarine waters and the rest of their life in both ocean and estuarine waters.

Other poorly understood sources of natural mortality for Atlantic menhaden are diseases and parasites. There is no information available concerning the extent of parasitism or its possible effect on survival. Studies described the incidence of ulcerative mycosis (UM), a fungal infestation which was observed in menhaden over much of their range in 1984 and 1985 and in a more restricted area in 1986. A large fish kill in Pamlico Sound, North Carolina in November, 1984 was associated with UM, but its primary effect may be to weaken fish, making them more susceptible to other causes of mortality, such as predation, parasites, other diseases, and low dissolved oxygen concentrations. The overall impact of UM on the 1984 and 1985 year classes could not be assessed, but it was not believed to be significant. However, other scientists believed that the mortality effects of a disease or other event must be "truly catastrophic" to be detectable.

Another source of natural mortality for Atlantic menhaden (and many other species) may be "red tide." The term refers to the color of water caused by the rapid multiplication ("bloom") of single-celled planktonic organisms called dinoflagellates, which produce a toxic compound. The toxin accumulates in the tissues of filter-feeding animals which ingest the dinoflagellate. An outbreak of red tide occurred along the coast of the Carolinas during November, 1987 - April, 1988 when Gulf Stream water containing the dinoflagellates was transported into coastal waters. Menhaden recruitment in Beaufort Inlet during this period was severely reduced.

A new species of toxic dinoflagellate was identified as the causative agent in a major menhaden kill in the Pamlico River, North Carolina, in May, 1991. Problems with toxic phytoplankton organisms may increase in the future since their appearance has been correlated with increasing nutrient enrichment in estuarine and coastal waters which are subject to increasing organic pollution.

An additional source of mortality are fish "kills" which occur when schools of menhaden enter enclosed inshore bodies of water in such large numbers that they consume all available oxygen and suffocate. The mean lethal dissolved oxygen concentration for menhaden has been reported to be 0.4 mg/l. Bluefish are known to follow (or even chase) schools of menhaden inshore, feeding on them, and may contribute to their mortality by preventing them from leaving an area before the oxygen supply is depleted. Oxygen depletion is accelerated by high water temperatures which increase the metabolic rate of the fish; at the same time, oxygen is less soluble in warm water. Menhaden which die from low oxygen stress can immediately be recognized by the red coloration on their heads caused by bursting blood capillaries. Just before death, the fish can be seen swimming very slowly in a disoriented manner just below the surface of the water. This is a common phenomenon which has been observed throughout the range of the species. Menhaden spotter pilots have reported menhaden "boiling up" from the middle of dense schools, and washing up on the beach, apparently from oxygen depletion within the school. This phenomenon was observed during December, 1979 in the ocean off Atlantic Beach, North Carolina. Other scientists reported a similar event off Core Banks, North Carolina, in December 1997. Other species are not nearly as susceptible simply because they do not enter enclosed inshore waters in such large numbers.