Although sodium and water reabsorption by the kidney plays a major role in maintaining body fluid homeostasis, the seasonal response of renal morphology and the factors involved in water and salt regulation are not well known, especially in reptiles. Eremias multiocellata is a typical desert-dwelling lizard. Here, we compared water and salt regulation of E. multiocellata in winter (hibernation), spring (emerging from hibernation), and summer (active) according to histomorphometry and the expression of genes such as those encoding aquaporins (AQP1, AQP2, AQP3), the Na+-Cl- cotransporter (NCC), the Na+-K+-2Cl- cotransporter (NKCC2), renin (Ren), angiotensin II receptor type 2 (AT2R), and endothelial nitric oxide synthase (eNOS) in the kidneys. The results showed that the area of Bowman's capsule and the glomerular density were lower in winter compared to summer and spring, and the lumen size of the DCT, PCT, and IS was greater in spring than in summer. Compared to summer and spring, the expression of AQP1, AQP3, NCC, NKCC2, Ren, and eNOS was significantly decreased in winter, whereas the expression of AQP2 and AT2R remained high. These results indicate that E. multiocellata balances its water budget via morpho-functional changes in different seasons. Although renal function was temporarily attenuated during winter, the regulation of aquaporins genes was not synchronous, indicating the complexity and particularity of water and salt regulation in desert lizards when facing the constraints of harsh environmental conditions, seasonal variations, and hibernation. These results will enrich the understanding of water and salt regulation mechanisms in desert reptiles.