The Western diet, which is typically high in saturated fatty acids (SFAs) and low in n-3 polyunsaturated fatty acids (PUFAs), has been identified as a factor contributing to the growing obesity rate. Long-term consumption of high-fat diets (HFDs) has also been associated with increased risk of chronic kidney disease. Therefore, we hypothesized that different fatty acids composition in HFDs would differentially affect renal microstructure and expression pattern of selected genes. Swiss-Webster male mice (n = 24) were fed a standard chow for mice (STD) or HFDs rich in SFAs, and rich in PUFA with a linoleic acid (LA) to α-linolenic acid (ALA) ratio of 14:1 (HR) or 5:1 (LR) for 3 months. We observed that both the SFA and HR groups had increased epithelial cell vacuolisation, collagenous tissue area and number of TUNEL-positive cells, accompanied by elevated Kim-1 expression in the kidneys. Sod1 and Cat were up-regulated, while Cox2 was down-regulated in the kidneys of HR mice when compared to the STD group. Both PUFArich HFDs down-regulated the Ren1 and Agt genes. The HR diet also caused an increased deposition of AQP2 in the basolateral membrane (BLM) and intracellular space of collecting duct (CD) cells. In both the HR and SFA groups, an increased expression of the Aqp3 gene and AQP3 protein in CD cells was observed. In conclusion, the findings suggest that higher levels of ALA in the HFD were associated with a reduction in the severity of renal tissue lesions. Diets rich in SFAs or LA have the potential to modify the renal mechanism of facultative urine concentration by altering the expression and/or distribution of AQP2 and AQP3 in the kidneys.