Reported estimates of CH4 emissions from ruminants and manure management are up to 2 times higher in atmospheric top-down calculations than in bottom-up (BU) inventories. We explored this discrepancy by estimating CH4 emissions of 2 dairy facilities in California with US Environmental Protection Agency (US EPA) methodology, which is used for BU inventories, and 3 independent measurement techniques: (1) open-path measurements with inverse dispersion modeling (hereafter open-path), (2) vehicle measurements with tracer flux ratio method, and (3) aircraft measurements with the closed-path method. All 3 techniques were used to estimate whole-facility CH4 emissions during 3 to 6 d per farm in the summer of 2016. In addition, open-path was used to estimate whole-facility CH4 emissions over 13 to 14 d per farm in the winter of 2017. Our objectives were to (1) compare whole-facility CH4 measurements utilizing the different measurement techniques, (2) compare whole-facility CH4 measurements to US EPA inventory methodology estimates, and (3) compare CH4 emissions between 2 dairies. Whole-facility CH4 estimates were similar among measurement techniques. No seasonality was detected for CH4 emissions from animal housing, but CH4 emissions from liquid manure storage were 3 to 6 times greater during the summer than during the winter measurement periods. The findings confirm previous studies showing that whole-facility CH4 emissions need to be measured throughout the year to estimate and evaluate annual inventories. Open-path measurements for liquid manure storage emissions were similar to monthly US EPA estimates during the summer, but not during the winter measurement periods. However, the numerical difference was relatively small considering yearly emission estimates. Manure CH4 emissions contributed 69 to 79% and 26 to 47% of whole-facility CH4 emissions during the summer and winter measurement periods, respectively. Methane yields from animal housing were similar between farms (on average 20.9 g of CH4/kg of dry matter intake), but CH4 emissions normalized by volatile solids (VS) loading from liquid manure storage (g of CH4 per day/kg of VS produced by all cattle per day) at 1 dairy were 1.7 and 3.5 times greater than at the other during the summer (234 vs. 137 g of CH4/kg of VS) and winter measurement periods (78 vs. 22 g of CH4/kg of VS), respectively. We attributed much of this difference to the proportion of manure stored in liquid (anaerobic) form, and suggest that manure management practices that reduce the amount of manure solids stored in liquid form could significantly reduce dairy CH4 emissions.