Reef manta (Mobula alfredi) populations along the east African coast are poorly studied and likely in decline. Identifying critical habitats for this species is essential for future research and conservation efforts. Dungonab Bay, a marine protected area and UNESCO World Heritage Site in Sudan, hosts the largest known reef manta aggregation in the Red Sea. Here we present approximately two years of passive acoustic telemetry monitoring data collected from 19 individuals and 15 strategically placed receivers. This data is used to quantify long-term residency and seasonal shifts in habitat use in Dungonab Bay. Additionally, acoustic telemetry combined with satellite telemetry was used to simultaneously track three mantas. On average, individual M. alfredi were detected within the array on 39% of monitored days. Detections were recorded throughout the year, though some individuals were occasionally absent from the receiver array for weeks at a time and generalized additive mixed models showed a clear seasonal pattern in detection probability. The highest probabilities occurred in boreal fall (~76% chance of detection) while the lowest occurred in boreal winter (~22%). Modeled biological factors, including sex and wingspan, had no influence on animal presence. Modeled environmental factors such as fraction of moon illuminated, sea surface temperature, and chlorophyll-a concentration were positively correlated with presence. Despite the high residency suggested by acoustic telemetry, satellite telemetry recorded one tagged individual moving at least 84 kilometers to the south towards Port Sudan. Although our satellite and acoustic telemetry data indicate excursions away from Dungonab, these individuals always returned and showed a strong degree of site fidelity. This study adds to growing evidence that M. alfredi are highly resident and site-dependent but display seasonal shifts in habitat selection that are likely driven by resource availability and the oceanographic features within their home range.