The biogeochemical processes responsible for production and emission of ammonia from stored liquid dairy manure are governed by environmental factors (e.g. manure temperature, moisture) and manure characteristics (e.g. total ammoniacal nitrogen concentration, pH). These environmental factors and manure characteristics vary spatially as a result of spatially heterogeneous physical, chemical, and biological properties of manure. Existing process-based models used for estimating ammonia emission consider stored manure as a homogeneous system and do not consider these spatial variations leading to inaccurate estimations. In this study, a one-dimensional compartmental biogeochemical model was developed to (i) estimate spatial variation of temperature and substrate concentration (ii) estimate spatial variations and rates of biogeochemical processes, and (iii) estimate production and emission of ammonia from stored scraped liquid dairy manure. A one-dimension compartmentalized modeling approach was used whereby manure storage is partitioned into several sections in vertical domain assuming that the conditions are spatially uniform within the horizontal domain. Spatial variation of temperature and substrate concentration were estimated using established principles of heat and mass transfer. Pertinent biogeochemical processes were assigned to each compartment to estimate the production and emission of ammonia. Model performance was conducted using experimental data obtained from National Air Emissions Monitoring Study conducted by the United States Environmental Protection Agency. A sensitivity analysis was performed and air temperature, manure pH, wind speed, and manure total ammoniacal nitrogen concentration were identified as the most sensitive model inputs. The model was used to estimate ammonia emission from a liquid dairy manure storage of a dairy farm located in Rockingham and Franklin counties in Virginia. Ammonia emission was estimated under different management and weather scenarios: two different manure storage periods from November to April and May to October using historical weather data of the two counties. Results suggest greater ammonia emissions and manure nitrogen loss for the manure storage period in warm season from May to October compared to the storage period in cold season from November to April. / Ph. D. / Dairy manure is a byproduct of dairy farming that can be used as a fertilizer to provide essential plant nutrients such as nitrogen, phosphorus, and potassium. However, manure can only be applied to crop lands in a certain time of the year during growing seasons. Further, discharge of dairy manure into natural environment is prevented by the environmental regulations. Therefore, manure storage structures are used to store liquid dairy manure until time permits for land application or use for other purposes. During the storage, liquid dairy manure goes through biological, chemical, and physical processes and release manure gases that are linked to deteriorate human and animal health and contribute to environmental pollution. Ammonia is one of the manure gases released to atmosphere from stored liquid dairy manure. Furthermore, release of ammonia from stored manure reduce nitrogen content and reduce fertilizer value of stored manure. Implementing control measures to mitigate ammonia emission is necessary to prevent ammonia emission and reduce nitrogen loss from stored manure. Deciding and applying of appropriate control measures require knowledge of the rate at which ammonia emission occurs and when ammonia emission occurs. Use of process-based models is one of the less expensive and reliable method for estimating ammonia emission from stored liquid dairy manure. Process-based model is a mathematical model that simulates processes related to ammonia production and emission from stored manure. Even though, there are several process-based models available for estimating ammonia emission from stored liquid dairy manure, these models do not fully represent the actual processes and conditions relevant to production and emission of ammonia. For instance, spatial variation of temperature and total ammoniacal nitrogen concentration within stored manure is not considered in existing process-based models. Therefore, in this study a new compartmental process-based model was developed for estimating these spatial variations and production and emission of ammonia from stored liquid dairy manure. The model uses weather data and manure management information as inputs for estimating ammonia emission and nitrogen loss. The performance evaluation of the compartmental process-based model revealed that air temperature, manure pH, wind speed, manure total ammoniacal nitrogen concentration are important model inputs for estimating ammonia emission from stored liquid dairy manure. The model was used to estimate ammonia emission from a dairy farm located in Rockingham and Franklin counties in Virginia. Results suggest greater ammonia emissions and manure nitrogen loss for the manure storage period in warm season from May to October compared to the storage period in cold season from November to April.