Cover and flare systems are suitable for dairy farms of all herd sizes and can help mitigate methane and other emissions while improving climate resiliency. Impermeable covers are gas-tight plastic membranes installed over the surface of a suitable manure storage structure to capture emissions and exclude rainwater. Biogas collected from under the cover can be combusted in a flare to reduce the potent greenhouse gas, methane, and to lessen potent carbon dioxide. Rainwater can be temporarily stored on the cover and used on-farm or pumped into an appropriate vegetated area.