We analyse the differences in the properties of the El Niño Southern Oscillation (ENSO) in a set of 17 coupled integrations with the flux-adjusted, 19-level HadCM3 model with perturbed atmospheric parameters. Within this ensemble, the standard deviation of the NINO3.4 deseasonalised SSTs ranges from 0.6 to 1.3 K. The systematic changes in the properties of the ENSO with increasing amplitude confirm that ENSO in HadCM3 is prevalently a surface (or SST) mode. The tropical-Pacific SST variability in the ensemble of coupled integrations correlates positively with the SST variability in the corresponding ensemble of atmosphere models coupled with a static mixed-layer ocean (“slab” models) perturbed with the same changes in atmospheric parameters. Comparison with the respective coupled ENSO-neutral climatologies and with the slab-model climatologies indicates low-cloud cover to be an important controlling factor of the strength of the ENSO within the ensemble. Our analysis suggests that, in the HadCM3 model, increased SST variability localised in the south-east tropical Pacific, not originating from ENSO and associated with increased amounts of tropical stratocumulus cloud, causes increased ENSO variability via an atmospheric bridge mechanism. The relationship with cloud cover also results in a negative correlation between the ENSO activity and the model’s climate sensitivity to doubling CO2.