Background <p>Rooftop rainwater harvesting is increasingly used for water supply, hence the need to understand how roofing materials, and long-time storage collectively influence the concentrations of metal in stored water and the potential human health risks. This study evaluated the temporal variation, storage-induced transformation, and non-carcinogenic health risks of metals in rooftop-harvested rainwater of Eleme, collected from aluminium (ALR), zinc (ZIR), asbestos (ASR) and ambient (AMB) roofs during early (April–June), peak (July–August), and receding (September–October) wet seasons. Fresh (i.e. Initially collected) and stored rainwater samples were analyzed for Al, Ca, Cu, Fe, K, Mg, Na, and Zn in mg L^− 1 using Atomic Absorption Spectrophotometer, alongside pH, microbial abundance, and exposure risks for adults and children.</p> Results <p>The early rainfall showed Al concentrations in fresh rainwater ranged from 0.033 (AMB) to 0.107 (ALR) in 2019 and 0.030 (AMB) − 0.096 (ZIR) in 2020. After storage, Al concentrations decreased sharply, showing maximum concentration of 0.076 (ALR) in 2019 and 0.063 (ALR) in 2020. As wet season enters its peak, freshwater Al levels increased in both years, commonly ranging between 0.033 (ALR) and 0.110 (ASR) while stored samples did not exceed 0.056 (ZIR). In the early wet season, Ca concentrations in the fresh rainwater ranged from 0.414 (AMB) − 0.937 (ALR) in 2019 and 2.468 (ALR) − 3.071 (ZIR) in 2020. Stored samples showed moderate increases, particularly in 2020, reaching up to 3.564 (AMB). Peak Ca levels occurred during this period, with the freshwater concentrations ranging from 1.323 (AMB) to 2.719 (ASR) in 2019 and 1.84 (AMB) − 2.149 (ASR) in 2020. After storage, there was a notable decrease in Ca concentrations, reaching 0.754 (AMB) − 1.649 (ASR) in 2019, but increased up to 5.438 (ASR). As late wet season set in, freshwater Ca concentrations declined to 0.296 (ASR) − 0.652 (ZIR) in 2019 and 1.345 (AMB) – 2.197 (ASR) in 2020, while stored samples remained elevated, particularly in 2020 (3.228 (AMB) − 5.899 (ASR)). Rainwater pH increased from acidic values (5.26–5.72) to neutral conditions (7.11–7.61) during storage, coinciding with 1–3 orders of magnitude increase in microbial counts. Health risk assessment showed higher ingestion risks for children, with Cu presenting the highest hazard quotient, whereas dermal risks remained negligible (HQ &lt; 1).</p> Brief conclusion <p>These results highlight water storage as a critical control point governing metal mobilization and exposure risk in rooftop-harvested rainwater.</p>