Carbonaceous and nitrogenous gases are produced during storage of livestock manure, with the magnitude of production being affected by the chemical properties of the manure and the physical conditions of storage. This lab-scale study quantifies the emission rates of ammonia (NH3), nitric oxide (NO), and greenhouse gases (GHG), i.e., methane (CH4), carbon dioxide (CO2), nitrous oxide (N2O), from biogas digester effluent (BDE) stored at different depths of 1.0, 1.5, and 2.0 m in dynamic emission vessels (DEVs). The selected storage depths were reflective of the typical depth range of on-farm BDE storage in China. The static storage was held at a relatively constant media temperature of 15°C and an air exchange rate of 11.5 air changes per hour (ACH) for 78 days. Each depth regimen was replicated four times using four DEVs (12 DEVs total). The results showed that the mean (±SE) daily gaseous emission rates per volume of BDE stored at 1.0, 1.5, and 2.0 m depths, in g gas m-3 d-1, were, respectively, 9.1 (±0.7), 10.1 (±0.6), and 10.1 (±0.4) for CH4 (p = 0.39); 38.0 (±2.2), 34.5 (±1.3), and 30.7 (±0.6) for CO2 (p < 0.05); 1.9 (±0.11), 1.3 (±0.08), and 0.9 (±0.03) for NH3 (p < 0.05); and 6.7 (±0.5) × 10-3, 5.0 (±0.8) × 10-3, and 3.4 (±0.2) × 10-3 for N2O (p < 0.05). Nitric oxide (NO) emissions were negligible. The overall GHG (CH4 + N2O + CO2) emissions were dominated by CH4, which accounted for more than 85% of the CO2-equivalent emissions for all three storage depths. The CH4 emissions peaked during the early storage period, with the first 20-day cumulative emissions accounting for 56% to 58% of the total 78-day storage emissions. The results reveal that storage of BDE at 2.0 m depth yielded lower CO2, NH3, and N2O emission rates but similar CH4 emission rates compared to the 1.0 and 1.5 m depths.