This study aims to evaluate the water balance of the crop mix of the Czech Republic and the tendencies of its development during the period 1961–2019. For calculating water deficits, methodology from ČSN 750434 (Czech technical standards) was used and on its basis, the deficits of the ten most frequently represented crops of the Czech Republic were calculated. These results were then put into the context of the development of precipitation totals and the development of average annual temperatures in the observed period. Furthermore, statistical tools were used for the identification of relationships between the observed variables and the tested hypotheses to verify the statistical significance of the observed changes. The results show that the overall irrigation deficit nearly doubled in Czech agriculture when comparing the averages for the periods 1961–1970 and 2010–2019. This change was evaluated as statistically significant. Furthermore, there were also statistically significant increases in water deficits in the cases of wheat, barley, rye, oats, legumes, and rapeseed. The sowing areas of the observed crops recorded statistically significant change in all cases. Only in the case of wheat, maize and rapeseed were there increases in sowing area, specifically 146%, 642.4%, and 1132.7%, respectively. For other crops, a decrease in sowing areas was observed. This finding points to decreasing commodity diversity in Czech agriculture, which, in combination with a high degree of intensification and selected agrotechnical practices, contributes to a lower retention capacity for the soil and landscape to retain water, which in turn influences the overall water balance of the Czech agrarian sector.