Seasonal flooding in Lagos metropolis disrupts infrastructure and livelihoods, yet seasonal-scale hazard characterization and early warning remain limited. This study mapped seasonal flood inundation and developed a Flood Early Warning System (FEWS) for Lagos using HEC-GeoRAS 10.2 for ArcGIS 10.2 and HEC-RAS 5.0.0 for 1993–2024. Daily rainfall from NIMET was analyzed for trends across DJF, MAM, JJA, and SON using the Mann-Kendall tau-b test. A 20-year return period flood was simulated in HEC-RAS, with outputs processed in ArcGIS to quantify hazard, risk, flow velocity, and runoff time. Model performance was validated against observed 2024 inundation extents using spatial agreement metrics. Rainfall exhibited a statistically significant decreasing trend toward the coast (Kendall’s tau-b = −0.52, p < 0.01), consistent with land–sea breeze circulation and suppressed convection over the Gulf of Guinea. Seasonal rainfall peaked in JJA (191.18 mm), followed by MAM (138.35 mm), SON (117.98 mm), and DJF (29.15 mm). Flood hazard and risk were highest in JJA and SON, with Alimosho, Amuwo Odofin, Eti Osa, Kosofe, and Ojo identified as priority LGAs. Flow velocities exceeded 3 m/s in 18% of high-risk zones, and runoff time exceeded 375 hrs in JJA in flat, low-gradient areas of Alimosho and Kosofe. Validation yielded 86% ± 5% spatial agreement with observed extents. A JJA-focused FEWS was developed using flood depth, extent, velocity, and lag time from runoff time. Warning thresholds of ≥1.0 m for onset, ≥3.0 m for warning, and >4.0 m for danger provide a 24–48 hr lead time. Applying a ±0.3 m SRTM DEM uncertainty buffer, this study provides the first seasonal-scale, validated FEWS for Lagos and identifies priority LGAs for drainage upgrades and floodplain zoning. The framework is replicable for flood risk reduction in rapidly urbanizing West African coastal cities.