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A process-level soil phosphorus (P) model including surface and subsurface components was developed and incorporated into the Integrated Farm System Model (IFSM). Preliminary verification indicated that the model accurately predicted soluble P losses but under-predicted total P losses. Simulations with IFSM analyzed the effects of manure handling and tillage systems on P loss from farms. Manure handling strategies that used six-month storage and application by injection decreased total P loss by 30% compared to daily surface application but decreased annual farm net return by about $30/cow. Use of conservation tillage and no-till systems reduced total P loss by 45% and 59%, respectively, with only small effects on farm profitability. Reduced tillage increased soluble P loss, suggesting that conservation and no-till systems should be combined with systems such as manure injection to reduce all forms of P loss.