Natural hydrogen can support the energy industry transitioning toward zero-carbon emitting fuels from the subsurface. However, the extent and exploitability of natural hydrogen resources is currently unknown. A key step towards discovering subsurface hydrogen accumulations is detecting natural hydrogen seeps. Here we present the first autonomous, multi-gas monitoring study of a natural hydrogen seep in Australia. Hydrogen seepage indicating substantial subsurface hydrogen generation was detected on the Yilgarn Craton in Western Australia. Significant fluctuations in hydrogen emissions at the site were observed across three seasons, such that hydrogen emissions were high after a dry summer but inhibited after rainfall (which led to high groundwater levels). Groundwater can act as a seasonal trapping mechanism in the near subsurface. Such inhibition of the natural hydrogen flux to the surface may lead to false negative readings in soil gas surveys after high rainfall and in low-lying areas. This work provides fundamental data for hydrogen exploration and therefore aids in the implementation of a large-scale hydrogen economy.