A combined strontium isotopic (87Sr/86Sr) and paleontological method is newly applied to a modern lagoon in Egypt's Nile River delta to test its applicability as a paleosalinity proxy. Analyses of 22 surficial samples collected throughout the lagoon include 81 Sr isotopic analyses of mollusks, foraminifera, ostracods, barnacles, bryozoans, serpulid worm tubes, pore water, and gypsum crystals. Two salinity groups are distinguished in each sample: a lower salinity group (∼1 ppt) mixed with a higher salinity group (∼3–10 ppt) that, respectively, are interpreted as the modern biocoenosis and an older relict fauna. The relict fauna denotes higher salinity conditions in the lagoon prior to closure of the Aswan High Dam (1964), and the modern fauna records freshening of the lagoon. Recent decreased salinity is a response to regulated Nile River flow and increased discharge into Manzala of fresh water via canals and drains. Quantification of this short-term salinity change holds promise for study of modern lagoons in other world settings, and may provide paleoclimatic information for older lagoon sequences in the Nile River delta and the geologic record.