This paper describes an agricultural model (Roth-CNP) that estimates carbon (C), nitrogen (N) and phosphorus (P) pools, pool changes, their balance and the nutrient fluxes exported from arable and grassland systems in the UK during 1800–2010. The Roth-CNP model was developed as part of an Integrated Model (IM) to simulate C, N and P cycling for the whole of UK, by loosely coupling terrestrial, hydrological and hydro-chemical models. The model was calibrated and tested using long term experiment (LTE) data from Broadbalk (1843) and Park Grass (1856) at Rothamsted. We estimated C, N and P balance and their fluxes exported from arable and grassland systems on a 5 km × 5 km grid across the whole of UK by using the area of arable of crops and livestock numbers in each grid and their management. The model estimated crop and grass yields, soil organic carbon (SOC) stocks and nutrient fluxes in the form of NH4-N, NO3-N and PO4-P. The simulated crop yields were compared to that reported by national agricultural statistics for the historical to the current period. Overall, arable land in the UK have lost SOC by −0.18, −0.25 and −0.08 Mg C ha−1 y−1 whereas land under improved grassland SOC stock has increased by 0.20, 0.47 and 0.24 Mg C ha−1 y−1 during 1800–1950, 1950–1970 and 1970–2010 simulated in this study. Simulated N loss (by leaching, runoff, soil erosion and denitrification) increased both under arable (−15, −18 and −53 kg N ha−1 y−1) and grass (−18, −22 and −36 kg N ha−1 y−1) during different time periods. Simulated P surplus increased from 2.6, 10.8 and 18.1 kg P ha−1 y−1 under arable and 2.8, 11.3 and 3.6 kg P ha−1 y−1 under grass lands 1800–1950, 1950–1970 and 1970–2010.