Carbonate-rich soils are common in many arid and semiarid areas. Many of them are cultivated, and agriculture is expanding by the spreading of irrigation. Although the soil mineral fraction has been usually considered little or not affected by agricultural management in the short term, increasing evidence suggests that this is not the case for carbonates in the tilled layer. The consequences of management can be intense and depend on the modifications induced in inorganic carbon cycling, which can result in gains or losses of total inorganic soil C, and in changes in its type (pedogenic vs. lithogenic), size and distribution. Net soil CO2 emissions and interactions with organic C cycle can be affected by these changes, thereby altering soil organic matter dynamics. This chapter summarizes the major observed effects of agricultural practices potentially altering soil carbonates, includes a case study in a newly irrigated area, and identifies the most important knowledge gaps and research perspectives.