Ammonia (NH3) and hydrogen sulfide (H2S) emissions from two manure storage basins of a 5600-cow western-US free stall dairy were measured intermittently over a two year period. Emissions were measured as the manure basin was being filled, as it was drying, and as the solids were removed (phases of handling). The dairy, located on an 11% north-south slope, was strongly influenced by local katabatic and anabatic winds. Path-integrated NH3 concentrations were measured in-situ using tunable diode lasers, while path integrated H2S concentrations were measured from continuously sampled air using pulsed-fluorescence technology. Emissions were determined from these concentration measurements combined with both turbulence (using a backward Lagrangian Stochastic model) and wind profile (using a vertical radial plume method model) measurements. Background NH3 (H2S) concentrations associated with emissions from other sources around the farm ranged from 25 ppb (4 ppb) to 206 ppb (9 ppb) during upslope flow and 108 ppb (4 ppb) and 300 ppb (35 ppb) during downslope flow. Emissions varied widely over the course of the manure storage period. Mean NH3 emissions from an actively filling basin ranged from 31 mg m-2s-1 to 48 mg m-2s-1. Mean NH3 emissions from an inactive basin ranged from 12 mg m-2s-1 as the manure dried to 60 mg m-2s-1 when dried manure sludge was removed from the basin. Mean H2S emissions ranged from 1 to 18 mg m-2s-1 as the manure filled and dried within a basin. The formation of a thick crust on the basins as they filled with manure decreased the NH3 (H2S) emissions by 13% (15%). The basin emitted 60% (91%) less NH3 (H2S) when it was no longer receiving fresh manure. The NH3 and H2S emissions were usually greater during downslope than upslope flow during most phases of manure handling. NH3 emissions were highly correlated with wind speed and only slightly with air temperature. H2S emissions were episodic, not correlated with wind speed, but associated with barometric pressure drops due to the passage of synoptic weather systems. The variation in emissions with phase of manure handling and storage indicates that determining the annual emissions from such dairies requires accounting for the duration of each manure handling and storage phase. The local downslope winds at this farm contributed significantly to the NH3 emissions.