Storage of livestock slurries is a significant source of methane (CH₄) and ammonia (NH₃) emissions to the atmosphere, for which accurate quantification and potential mitigation methods are required. Methane and NH₃ emissions were measured from pilot‐scale cattle slurry (CS) and pig slurry (PS) stores under cool, temperate, and warm conditions (approximately 8, 11, and 17°C, respectively) and including two potential mitigation practices: (i) a clay granule floating cover (PS) and (ii) slurry acidification (CS). Cumulative emissions of both gases were influenced by mean temperature over the storage period. Methane emissions from the control treatments over the 2‐mo storage periods for the cool, temperate, and warm periods were 0.3, 0.1, and 34.3 g CH₄ kg⁻¹ slurry volatile solids for CS and 4.4, 20.1, and 27.7 g CH₄ kg⁻¹ slurry volatile solids for PS. Respective NH₃ emissions for each period were 4, 7, and 12% of initial slurry N content for CS and 12, 18, and 28% of initial slurry N content for PS. Covering PS with clay granules reduced NH₃ emissions by 77% across the three storage periods but had no impact on CH₄ emissions. Acidification of CS reduced CH₄ and NH₃ emissions by 61 and 75%, respectively, across the three storage periods. Nitrous oxide emissions were also monitored but were insignificant. The development of approaches that take into account the influence of storage timing (temperature) and duration on emission estimates for national emission inventory purposes is recommended.Core Ideas: Gaseous emissions from livestock slurry storage are strongly influenced by storage temperature. Slurry acidification is an effective treatment to reduce CH₄ and NH₃ emissions. Covering with a layer of clay granules is effective at reducing NH₃, but not CH₄, emission. Methane conversion factors in national inventories should account for storage timing and duration.

Cattle and pig manure contain useful mineral nutrients (N, P, and K) and are therefore used as organic fertilizer. However, excessive applications of manure can cause environmental problems and threaten animal and human health because these materials also hold significant amounts of heavy metals, particularly Cu and Zn. To assess the potential risk due to the increased concentrations of heavy metals (Cu, Mn, Zn, and Cr) in a harvested crop, two maize hybrids were grown in pots on four different soils with three different fertilisers (urea, pig manure, and cattle manure). Both soil and manure characteristics influenced the heavy metal concentrations in the plant shoots. Organic fertilisation strongly interacted with the soils and, in general, reduced the shoot content of Cu, Mn, and Zn. A preliminary assessment of the heavy metal balance of the agricultural systems based on the intensive livestock production and maize cultivation showed that the potential soil enrichment of the long-term application of livestock manure arises mainly from the application of pig slurries that have a high content of Cu and Zn. The time required to apply an amount of metal that is equal to the initial soil content is 60–300 years for Zn and 240–450 years for Cu, depending on the soil type and the initial heavy metal content.