We use a state-of-the-art 3-dimensional coupled model to investigate the relative impact of long term variations in the Holocene insolation forcing and of a freshwater release in the North Atlantic. We show that insolation has a greater effect on seasonality and La Niña events and is the major driver of sea surface temperature changes. In contrast, the variations in precipitation reflect changes in El Niño events. The impact of ice-sheet melting may have offset the impact of insolation on El Niño Southern Oscillation variability at the beginning of the Holocene. These simulations provide a coherent framework to refine the interpretation of proxy data and show that changes in seasonality may bias the projection of relationships established between proxy indicators and climate variations in the east Pacific from present day records.