Dairy farming systems have rapidly intensified over the past several decades in many world regions. One of the main challenges in these intensive dairy farming systems is managing manure in a way that benefits agricultural production while minimizing environmental impacts. This research reviewed potential gaseous emissions (mainly ammonia, methane and nitrous oxide) from different manure management facilities, and developed a flexible modular manure management (FarmM3) model to quantify the flows and losses of nutrient from various manure management systems. Further, we explored how manure management approaches and the integration of crop and dairy production affect nutrient use efficiency and circularity at the whole farm level. The study emphasized the importance of improving manure management through multiple measures and integrating crop and dairy production within or between farms for sustainable dairy farming. These findings provide valuable insights for farmers and policy makers to reduce nutrient losses and improve nutrient circularity in intensive dairy farming systems.