Abstract A simple computer model to predict nitrogen (N) losses from anaerobic manure storages was developed and validated with both laboratory and literature data. Using the model, we investigated the effects of temperature, pH, and loading rate on N losses from bottom-loaded and top-loaded manure storages. Bottom-loaded storages provided good N conservation (less than 15% loss) under all conditions studied, whereas the top-loaded storages had a wide variation in N losses (3–60% ammonia loss). At low temperature, low pH, and/or high loading rate, the top-loaded storages conserved N almost as well as the bottom-loaded storages. In anaerobic storages, diffusion limits ammonia movement in the storage and possibly explains why bottom-loaded storages provide excellent N conservation.