Skeletal calcareous soils refer to soils consisting of skeletal remains of marine organisms. Although calcareous deposits are prevalent along coastal plains throughout the world, there is no study which investigates their behavior in unsaturated conditions. In these conditions, soil-water retention capacity is a fundamental parameter in relation to many geotechnical, environmental, and agricultural aspects. Water retention capacity of a soil is expected to be influenced by intra-particle pores unique to calcareous soils. Scanning electron microscopy (SEM) and mercury intrusion porosimetry (MIP) used in the current study clearly revealed this special microstructural characteristic. To study water retention and hydraulic hysteresis behavior of skeletal calcareous soil (obtained from the Hormuz Island of Iran) compared with a reference silicate soil (obtained from the Netherlands), a series of tests were conducted using pressure plate and controlled-suction oedometer apparatuses. Test results showed that in similar grain-size distribution of these soils, water retention curves of calcareous and silica soils are almost the same in low suctions, but calcareous soil retains more water at higher suctions due to its intra-particle voids. In addition, owing to these microstructural pores, ratio of Sr reduction on wetting path of a hysteresis loop was found to be more for calcareous soil than for silicate soil. Besides, to find and/or modify a prediction method for water retention curve of calcareous soil with acceptable accuracy, several existing pedotransfer functions were evaluated. Results showed that models proposed by Zapata et al. (Geotech Spec Publ 99:84–124, 2000) and Saxton et al. (Soil Science Society of America Journal 50(4): 1031–1036, 1986) after some simple modifications provide accurate estimations for water retention curve of calcareous soils.