Biodiversity is widely recognized as a key factor in determining ecosystem multifunctionality (EMF), as demonstrated in both experimental and theoretical studies. However, its role in maintaining EMF in natural ecosystems remains uncertain, since various environmental drivers, alongside biodiversity, can influence EMF and potentially complicate the empirical biodiversity-EMF relationship. Additionally, the effects of both environmental drivers and biodiversity on EMF likely vary across temporal scale, making the biodiversity-EMF relationship potentially scale-dependent. To address these issues, we conducted a biweekly sampling in a subtropical reservoir to collect nine-year time series of microbial diversity, various biotic and abiotic environmental factors, and EMF based on 31 functions related to microbial carbon utilization. By analyzing inter-annual, seasonal, and short-term components of the time series, our findings reveal that biodiversity consistently enhances EMF across different temporal scales, contrasting to distinct environmental factors that exert significant impacts only at specific scales. Specifically, precipitation, temperature, and phosphate were the dominant drivers of EMF at short-term, seasonal, and inter-annual scales, respectively, while their influence became diminished at other scales. Our results highlight biodiversity as a scale-invariant pillar in sustaining EMF, underscoring the importance of biodiversity conservation to safeguard EMF amid multifaceted environmental changes.