This paper presents the qualitative and quantitative characteristics of microstructures of Neogene clays from Warsaw, Poland. Scanning Electron Microscope (SEM) studies were used for the microstructural analysis of natural clays and clay pastes. Qualitative microstructural changes were observed: from a honeycomb microstructure for the initial clay paste to a turbulent microstructure for the dried paste. It was also noticed that water loss caused by the increase of the suction pressure had a significant impact on the microstructural transformations. Significant changes in the quantitative values of the pore space parameters were also observed. Increase of suction pressure and water loss caused a decrease in porosity and changes in the values of morphometric parameters, such as pore distribution; for example, a significant increase of the number of pores of 0−10 μm size and changes in the geometric parameters of the pore space were noticed with the increase of suction pressure. The pore space with larger isometric pores was modified into a pore space with the dominance of small anisometric and fissure-like pores. The increased degree of anisotropy from a poorly-oriented to a highly-oriented microstructure was also observed. After rapid shrinkage the reduction in the number of pores, maximum pore diameter, and total pore perimeter was recorded. The process of rapid water loss induced the closure of very small pores. A similar effect was observed during the increase of the suction pressure, where the closure of pore space of the clay pastes was observed very clearly.