Intensive agricultural practice leads to periodic accumulation of enormous amounts of liquid manure (slurry) from animal husbandry, and large quantities of environmentally hazardous ammonia and methane are emitted from the manure storages. Floating surface crusts have been suggested to harbour methane oxidizing bacteria (MOB) and are known to accumulate nitrite and nitrate, indicating the presence of ammonia oxidizers (AOB). We have surveyed six manure tanks with organic covers to investigate the prevalence of MOB and AOB and to link the potential activity with physical and chemical aspects of the crusts. PCR targeting the unique methane and ammonia monooxygenases were applied together with FISH to detect the presence of the two bacterial groups. Potential activity was assessed by short term slurry incubations of crust samples while monitoring NO2- production or CH4 consumption. Crusts were characterized with respect to O2 availability by in situ profiling with electrochemical microsensors. Results show that oxygen penetration increased from few micrometers up to several centimetres with crust age. AOB and ammonium oxidation are ubiquitously present in well-developed manure crusts whereas MOB were only present in old crusts which then could have very high potential rates of methane oxidation. In old crusts the potential rates of both processes were in the range of reported fluxes of CH4 and NH3 from slurry storages without surface crust. Results indicate that with respect to NH3 and possibly also CH4 emission mitigation, an organic surface crust can be effective if populations of MOB and AOB are allowed to build up.