Ammonia emissions from two contrasting seabird colonies in Scotland were measured, based on the determination of atmospheric concentrations downwind of the colonies. Atmospheric concentrations of ammonia (NH 3 ) across the downwind plume were compared with the inverse application of a Gaussian dispersion model (ID) to calculate the modelled NH 3 emission that would generate the measured cross-wind-integrated plume concentration. In parallel, a tracer gas (sulphur hexafluoride, SF 6 ) was released from the colonies with air samples taken to allow determination of SF 6 concentrations. On the basis of the known emission rate of SF 6 , the magnitude of ammonia emissions was estimated by the cross-wind-integrated tracer ratio (TR) of NH 3 /SF 6 concentrations. Coupled with data on annual bird attendance, the measurements indicate annual emissions from the Isle of May and the Bass Rock of 18 and 132 tonnes NH 3 -N year −1 , respectively. The measured NH 3 emissions were compared with estimates of seabird nitrogen excretion to estimate the proportion of excreted N that is volatilised as NH 3 (F Nr ). The emission estimates of the two methods compared favourably, giving 4 and 6 kg NH 3 -N h −1 (F Nr = 15%) for the Isle of May for the ID and TR methods, respectively, and 21 and 25 kg NH 3 -N h −1 (F Nr = 50%) for the Bass Rock for the ID and TR methods, respectively. The results provide the first measurement-based estimates to allow regional up scaling of ammonia emissions from seabirds.