We investigate the impact of nanoparticle roughness on the phase behaviour of suspensions in models of calcium carbonate nanoparticles. We use a Derjaguin approach that incorporates roughness effects and interactions between the nanoparticles modelled with a combination of DLVO forces and hydration forces, derived using experimental data and atomistic molecular dynamics simulations, respectively. Roughness effects, such as atomic steps or terraces appearing in mineral surfaces result in very different effective inter-nanoparticle potentials. Using stochastic Langevin Dynamics computer simulations and the effective interparticle interactions we demonstrate that relatively small changes in the roughness of the particles modify significantly the stability of the suspensions. We propose that the sensitivity of the phase behavior to the roughness is connected to the short length scale of the adhesive attraction arising from the ordering of water layers confined between calcite surfaces. Particles with smooth surfaces feature strong adhesive forces, and form gel fractal structures, while small surface roughness, of the order of atomic steps in mineral faces, stabilize the suspension. We believe that our work helps to rationalize the contrasting experimental results that have been obtained recently using nanoparticles or extended surfaces, which provide support for the existence of adhesive or repulsive interactions, respectively. We further use our model to analyze the synergistic effects of roughness, pH and ion concentration on the phase behavior of suspensions, connecting with recent experiments using calcium carbonate nanoparticles.