Energy produced by controlled oxidation of hydrogen in a fuel is sometimes referred to the ideal form of energy conversion since the process produces no soot, oxides of nitrogen, sulfate, or carbon dioxide. However, releases of H2 in the process could have significant negative environmental consequences. H2 is a trace constituent of the atmosphere (0.5 ppmV). Tromp et al (2003) estimate that if all gasoline and oil-based combustion were replaced by hydrogen fuel cells, the expected losses during commercial transport of H2 would contribute 60-120 Tg of H2 per year to the atmosphere. Given the very low natural concentrations of H2 in the atmosphere, this amount could have negative environmental consequences. Tromp et al (2003) suggest this could (1) decrease OH concentrations in the troposphere and increase OH in the stratosphere, which increases the lifetimes of CH4 and CO (both greenhouse gases) in the stratosphere and decrease them in the troposphere, (2) increase H2O in the mesosphere (above the stratosphere) and hence increase the occurrence of noctilucent (very high altitude) clouds thereby increasing reflection of solar radiation, and (3) fertilize soil microbes, since H2 is a microbial nutrient, with unknown long-term consequences.
Reference
Tromp, T, K., R.-L. Shia, M. Allen, J. M. Eiler, and Y. L. Yung, 2003: Potential environmental impact of a hydrogen economy on the stratosphere. Science 300, 1740-1742.