Agricultural systems integrating perennial grass-legume pastures in rotation with grain crops sustain high crop yields while preserving soil organic carbon (Cs) with low nitrogen (N) fertilizer inputs. We hypothesize that Cs saturation in the topsoil may explain the favorable C and N cycling in these systems. We tested this hypothesis by evaluating and simulating three contrasting crop and pasture rotational systems from a 20-year no-till experiment in Treinta y Tres, Uruguay. The systems were: 1) Continuous annual cropping (CC); 2) crop-pasture rotation with two years of crops and four years of pastures (CP); and 3) perennial pasture (PP). Using the Cycles agroecosystems model, we evaluated the inclusion or exclusion of a Cs saturation algorithm. The model simulated forage, soybean, and sorghum grain yields correctly, with low root mean square error (RMSE) of 1.5, 0.7 and 1.0 Mg ha−1, respectively. Measurements show Cs accretion and Cs decline for the first and second half of the experiment, respectively. The Cs accretion rate was highest for PP, while the Cs decline was highest for CC (1.3 vs −0.6 Mg ha−1 y−1 of C). The model captured this Cs dynamics and performed better when using the Cs saturation algorithm than when excluding it (RMSE 4.7 vs 6.8 Mg C ha−1 and relative RMSE of 14% and 21% for the top 15-cm). The model with saturation simulated subsoil Cs distribution with depth well, and simulated faster N turnover and greater N availability for the subsequent grain crop in CP vs CC. The results suggest that Cs saturation, and by extension soil organic N saturation, underpin the sustainability of crop-pasture rotations, and that modeling Cs saturation dynamics can be critical to reliably simulate complex crop-pasture rotational systems.