Our objective was to determine the sustainability for 8 crop rotation sequences of 3-yr rotations in a long-term (25-yr) well-managed organic dairy farm in Maine. A medium-sized organic dairy farm was simulated with the Integrated Farm System Model (version 3.6) to evaluate crop rotation (management) effects on crop performance, environmental impacts and profitability. The 9 cropping strategies included continuous ryegrass/red clover (continuous grass), corn harvested early followed by winter wheat (corn-wwheat-grass), corn followed by spring wheat (corn-swheat-grass), ryegrass/red clover rotated with winter wheat (grass-wwheat-grass), ryegrass/red clover in rotation with spring wheat (grass-swheat-grass), soybean rotated with both winter wheat (soybean-wwheat-grass) and spring wheat (soybean-swheat-grass), corn double cropped (corn-corn-grass) and soybean followed by corn (soybean-corn-grass). Wheat was harvested as a cash crop in all simulated years and sold at an organic premium price. All rotations were in long rotation with perennial ryegrass/red clover over the 3 yr period. When the continuous grass-based system was simulated, farm net return was higher ($742.15/cow). Under crop rotation, the option of growing and selling winter wheat instead of spring wheat improved farm profitability when the results were compared with other wheat cropping rotations. The higher winter wheat yields for soybean-wwheat-grass resulted in 7% more income from feed sales ($1,027) and 1% more in total revenue ($1,065). Also, winter wheat should be encouraged to reduce soil nutrient accumulation, particularly soybean replaced with cash crop wheat (soybean-wwheat-grass). Here the major reductions in nutrient flows were a 0.8 kg/ha/yr decrease in both P runoff and leachate losses and K accumulation (−17%); there was also a 4% reduction in water footprint (kg/kg FPCM). Use of corn harvested as silage in place of grass or/and soybean in the first year or winter/spring wheat in the second year provided relatively less profitability to the farm. In general, there were lower economic and more favorable environmental benefits to shifting land from continuous grass-based production to specified small grain cropping rotations.