Motivation behind the spring whale shark (Rhincodon typus) aggregation in Al-Lith, on the Saudi Arabian coast of the South Central Red Sea, is uncertain. A plausible hypothesis is that whale sharks gather to feed on high prey density, leading to questions about the cause of the prey density. A bottom-up process fueled by nutrient input or accumulation from physical advection could create a peak in prey biomass. Wastewater discharged from an aquaculture facility could affect productivity or provide a chemosensory cue for whale sharks. Yet, basic physico-biological oceanography of this region is unresolved. Monthly profiles, long-term moorings, and spatial surveys were used to describe the temporal variability of potential prey biomass and water masses in this region for the first time. Plankton abundance of individuals larger than ~0.7 cm did not peak during whale shark season. Rather, a decrease coinciding the trailing end of whale shark detections was observed. Sites 180 m apart had differences in acoustic backscatter, suggesting small-scale biomass patchiness, supporting the small-scale variability in whale shark habitat selectivity. Red Sea Deep Water, a nutrient-rich water mass formed in the northern Red Sea, appeared in July at the same time the Tokar wind jet from the Sudanese mountain gap is the highest. Gulf of Aden Water, a nutrient-rich water mass from the Indian Ocean, arrived as episodes from May to September, contrary to previous expectations that the water arrives continuously. It is unlikely that these natural nutrient sources are directly responsible for the high prey density attracting the whale sharks. The aquaculture plume, observed at the aggregation site, had a distinct seasonality from the ambient waters. The plume’s highest salinity (>48) approached the extreme limits of coral tolerances. Nutrient concentrations (nitrate, nitrite, phosphate, silica), suspended particulate matter, phytoplankton biomass, bacteria and cyanobacteria cell counts, total nitrogen, and relative abundance of genera associated with opportunistic pathogenic species (e.g., Arcobacter) were significantly higher in the plume. This study was the first to estimate the nutrient flux and spatial variability of the aquaculture plume.