The trace concentration of H in most ecosystems after the Earth's oxidation has long caused the neglect of hydrogenotrophic denitrification for nitrogen loss. Here, we find that the interspecies hydrogen transfer between cyanobacteria and symbiotic bacteria within cyanobacterial aggregates is an undiscovered pathway for nitrogen loss. Cyanobacteria in aggregates can actively generate H under the diel cycle as an electron donor for neighboring hydrogenotrophic denitrifiers. The hydrogenotrophic denitrification in engineered cyanobacterial aggregates accounts for a nitrogen removal rate of 3.47 ± 0.42 mmol l day. This value is nearly 50% of the heterotrophic denitrification rate, which far exceeds the general concept of the trace role. We find that H-evolving cyanobacteria and hydrogenotrophic denitrifiers coexist in 84% of the 63 globally distributed cyanobacterial aggregates, where bloom colonies and phototrophic mats from hot springs are identified as potential hotspots. We suggest that interspecies hydrogen transfer within cyanobacterial aggregates is possibly responsible for the excessive nitrogen loss rate during cyanobacterial blooms where cyanobacterial aggregates persist.