Cyanobacteria Rule Egypt’s Lake Manzala as Nutrient Pollution Reshapes Algal Seasons

A year-long survey of Egypt’s largest brackish lagoon has revealed a microbial world in flux, where the tiny photosynthetic organisms that underpin one of the country’s most important fisheries are being reshuffled by pollution, salinity, and the seasonal push and pull of the Mediterranean Sea. Researchers from Damietta University monitored six sites along the northern side of Lake Manzala throughout 2022, tracking water chemistry and phytoplankton communities across summer, autumn, winter, and spring. Their findings, published in the journal Discover Ecology, paint a picture of a highly eutrophic ecosystem in which cyanobacteria dominate in cell numbers and biomass, and where the healthiest water is found precisely where the sea flushes into the lake.

Lake Manzala occupies the northeastern corner of the Nile Delta, stretching roughly 60 kilometers along the Mediterranean coast between the Suez Canal and the Damietta branch of the Nile, with an average depth of just 1.15 meters. For decades the lake received nearly 98 percent of its annual inflow from six major drains, most notably Bahr El-Baqar, carrying agricultural runoff, sewage, and industrial effluent. Yet recent national restoration projects between 2017 and 2022 have focused on re-opening the narrow marine inlets, called Boughaz, that connect the lake to the Mediterranean. Dredging of these channels has increased tidal flushing, shifting salinity profiles and creating a striking north-south gradient: the northern sites experience relatively higher salinity and lower nutrient concentrations, while the southern sectors remain fresh, fertilizer-laden, and contaminated with toxic elements.

The study team, Mohamed Deyab and Fatma Ward, sampled six representative locations: Towall Ibrahim, El Nafft, Abo El-Ross, El-Deiba, Shatta, and El-Rattama. Physicochemical measurements revealed that most sites maintain a slightly alkaline pH, with values ranging from 7.6 in autumn at Towall Ibrahim to 8.5 in summer at El-Deiba. Temperature peaked at 30.1 degrees Celsius in summer at Towall Ibrahim and dropped to 14.5 degrees in winter at Abo El-Ross. Salinity emerged as the defining variable separating the sites. El-Deiba, the primary connection point between the lake and the Mediterranean, recorded the highest salinity in every season, ranging from 24.5 to 31.5 parts per thousand, indicating near-marine conditions. By contrast, Towall Ibrahim, Shatta, and Abo El-Ross showed salinity as low as 2.2 parts per thousand, reflecting their dependence on freshwater drainage.

Nutrient data told a more troubling story. Towall Ibrahim recorded the highest total nitrogen, up to 7.2 milligrams per liter, and total phosphorus, up to 1.50 milligrams per liter, during summer, while El-Deiba consistently reported the lowest concentrations of both. Dissolved oxygen followed a predictable seasonal pattern, reaching winter maxima between 6.5 and 9.4 milligrams per liter and falling to summer minima as low as 2.8 milligrams per liter, since colder water holds more dissolved gas. The contrast between sites was stark: high oxygen near the marine-flushed El-Deiba, chronically low oxygen at Towall Ibrahim and Abo El-Ross, where decomposition of organic matter from drainage water depletes the supply. When the researchers calculated the Water Quality Index, El-Deiba emerged as the best site with values between 22 and 45, while Towall Ibrahim was the most degraded, averaging 154.2. All sites showed their worst water quality in summer and their best in winter.

Carlson’s Trophic Status Index, computed from chlorophyll-a and total phosphorus, confirmed that the northern lake is highly eutrophic at most sites. The highest value, 94.5, was recorded in summer at Towall Ibrahim, coinciding with a chlorophyll-a concentration of 140 micrograms per liter, placing the site firmly in the hypereutrophic category. Even the lowest value, 64.08, recorded in winter at El-Deiba, falls within the eutrophic range, suggesting the lake sits perilously close to hypereutrophic conditions despite marine flushing. The authors note that calculating the index from chlorophyll and phosphorus rather than water transparency avoids the inaccuracies that arise in shallow, turbid systems where suspended sediments, not algae, often control light penetration.

Against this chemical backdrop, the phytoplankton community told its own seasonal story. The team identified 32 species across four phyla: 17 bacillariophytes, or diatoms; 10 cyanophytes, or blue-green bacteria; 4 dinophytes; and a single xanthophyte. Diatoms contributed the greatest number of species, but cyanobacteria dominated in sheer cell numbers and biomass throughout most of the year. The tiny picocyanobacterium Synechocystis salina proved to be the most abundant organism year-round, peaking in spring with 156.9 million cells per liter at El-Rattama and a biomass of 12.589 milligrams per liter. Seasonal species counts collapsed in summer, when only 7 species were recorded, compared with 21 in autumn, 12 in spring, and just 4 in winter. Diatoms reached their own maximum in autumn, hitting 4.58 million cells per liter and 2.313 milligrams per liter of biomass at El-Rattama, while dinoflagellates peaked at 38.09 million cells per liter in autumn and 10.78 milligrams per liter of biomass in winter at the same site.

The autumn diatom bloom, the authors explain, is a classic temperate-lake mechanism playing out in a delta lagoon. During hot months, the shallow water column can become weakly stratified by temperature. As air temperatures drop in autumn, surface water cools, densifies, and sinks, creating vertical mixing that hauls nutrient-rich sediments and dissolved silica from the lake bottom up into the sunlit zone where diatoms live. Diatoms, which build their glassy frustules from silica, also prefer cooler conditions than the brutal heat of an Egyptian summer. The dominance of Nitzschia at only a single autumn station in this study contrasted with earlier surveys that found the genus across the entire lake, a discrepancy the researchers attribute to shifts in nutrient loading and organic discharge between study periods, as well as competitive exclusion by seasonally dominant cyanobacteria at other stations.

The prevalence of Synechocystis salina carries ecological consequences that ripple up the food web. This organism is a supremely adaptable competitor, capable of re-tuning its photosynthetic pigment antenna in response to changing light, and previous work has documented its tolerance of heavy metals and its capacity to strip organic load from wastewater, traits that help it thrive in polluted, saline conditions. But dominance by such small cyanobacteria creates what the authors call a trophic bottleneck: energy becomes trapped at the base of the food web in cells of poor nutritional quality for zooplankton, potentially suppressing the small fish populations that larger commercial species depend upon. This matters enormously in a lake that has averaged roughly 64 thousand tonnes of annual fish landings over the past decade, with cichlid tilapia making up about 70 percent of the catch. Licensed fishing activity on the lake has already collapsed dramatically, from 2,748 boats and 2,711 fishermen in 2021 to just 485 boats and 1,016 fishermen in 2022.

Diversity metrics revealed a clear seasonal signature. The Shannon-Wiener diversity index and species richness peaked in autumn at nearly every site except Shatta, which remained at persistently low diversity, with index values between 0.11 and 0.24. Abo El-Ross swung from a single genus in winter to the most diverse site in autumn, reaching an index of 1.47. Statistical analysis showed that species richness correlated significantly and positively with temperature and dissolved oxygen, but significantly and negatively with pH, total nitrogen, total phosphorus, and chlorophyll-a. Salinity showed a moderate positive correlation with species richness and negative correlations with nutrients and chlorophyll. Total nitrogen and total phosphorus were almost perfectly correlated with each other and with chlorophyll-a, confirming that nutrient loading is the primary engine of algal biomass in the lake. Two-way ANOVA demonstrated that both site and season significantly shaped cell numbers and biomass, with season exerting the stronger effect.

The broader message is unambiguous: despite restoration efforts that have reconnected the lake to the sea, the northern side of Lake Manzala remains under severe environmental stress, particularly at Towall Ibrahim and Abo El-Ross, where nutrient concentrations fuel summer algal blooms and depress oxygen. The relative health of El-Deiba demonstrates that enhanced marine exchange can dilute pollutants and support a more diverse, marine-influenced community, offering a template for future management. The authors conclude that phytoplankton in the lake respond directly to shifts in temperature, salinity, and nutrient availability, and they call for intensified restoration efforts alongside further research into the competitive interactions among phytoplankton species. For a lake that feeds millions of Egyptians with inexpensive fish, the microscopic community at its base may be the most important early warning system the country has.

Subject of Research: Seasonal dynamics of phytoplankton communities and water quality in the northern side of Lake Manzala, Egypt

Article Title: Seasonal variations in phytoplanktonic community structure at the northern side of Lake Manzala, Egypt

Article References: Deyab, M., & Ward, F. (2026). Seasonal variations in phytoplanktonic community structure at the northern side of Lake Manzala, Egypt. Discover Ecology, 2(1), Article 17. https://doi.org/10.1007/s44396-026-00035-y

Image Credits: AI Generated

DOI: 10.1007/s44396-026-00035-y

Keywords: Lake Manzala, phytoplankton, cyanobacteria, eutrophication, water quality, Mediterranean, Egypt, Synechocystis salina, diatoms, nutrient pollution, biodiversity, fisheries