The aim of the current study was to evaluate the productive capacity of the phytoplankton community and other environmental variables in the estuarine area of Suape; while considering the constant morphological, sedimentological and hydrological changes, the site has been facing due to the implementation and expansion of an industrial and port complex. The study comprised 6 campaigns: 3 in the dry season and 3 in the rainy season. Water samples were collected from the surface layer of the internal and external portions of the estuarine bay during low spring tides. The salinity ranged from 32.20 to 37.10, the water temperature ranged from 26.60˚C to 29.40˚C, and the oxygen saturation rate ranged from 58.5% to 114.5%. There was significant seasonal variation. The nitrite concentration was higher during the rainy season, whereas the ammonia concentration was higher during the dry season; the higher ammonia concentration helped increase chlorophyll-a levels and rates of primary productivity, which ranged from 0.02-2.45 mg•m −3 and from 0.34 to 4.32 mg•C•m −3 •h −1 , respectively. Chlorophyll-a < 20 μm was the fraction of biomass most commonly present in the estuarine ecosystem, accounting for 88.6% of the chlorophyll-a-containing biomass, and this reflected the low nutrient content in the water and indicated that the area was free from eutrophication processes. The decrease of rainfall during the sampling months and the anthropogenic changes in the environment led to reduced continental contributions, increased marine interference, nutrient dilution and loss of phytoplankton production capacity in Suape Bay, which severely damaged other trophic links in the ecosystem.