Long-term decreases in the incident total radiation and water clarity might substantially affect the underwater light environment in aquatic ecosystems. However, the underlying mechanism and relative contributions of radiation dimming and decreasing water clarity to the underwater light environment on a national or global scale remains largely unknown. Here, we present a comprehensive dataset of unprecedented scale in China’s lakes to address the combined effects of radiation dimming and decreasing water clarity on underwater darkening. Long-term total radiation and sunshine duration showed 5.8% and 7.9% decreases, respectively, after 2000 compared to 1961–1970, resulting in net radiation dimming. An in situ Secchi disk depth (SDD) dataset in 170 lakes showed that the mean SDD significantly decreased from 1.80 ± 2.19 m before 1995 to 1.28 ± 1.82 m after 2005. SDD remote sensing estimations for 641 lakes with areas ≥ 10 km² showed that SDD markedly decreased from 1.26 ± 0.62 m during 1985–1990 to 1.14 ± 0.66 m during 2005–2010. Radiation dimming and decreasing water clarity jointly caused an approximately 10% decrease in the average available photosynthetically active radiation (PAR) in the euphotic layer. Our results revealed a more important role of decreasing water clarity in underwater darkening than radiation dimming. A meta-analysis of long-term SDD observation data from 61 various waters further elucidated a global extensive underwater darkening. Underwater darkening implies a decrease in water quality for potable water supplies, recession in macrophytes and benthic algae, and decreases in benthic primary production, fishery production, and biodiversity.