Maternal obesity during pregnancy has a detrimental impact on offspring renal development and function. This is pertinent to Indigenous Australians as they are twice as likely as non‐Indigenous Australians to develop chronic kidney disease (CKD). The aim of this study was to examine whether there was an association between maternal adiposity and fetal kidney growth in late gestation (>28 weeks) and kidney function in infants, <2.5 years of age, from the Gomeroi gaaynggal cohort. Pre‐pregnancy body mass index (BMI) was recorded at the first prenatal visit and maternal adiposity indicators (percent body fat and visceral fat area) measured at >28 weeks gestation by bioelectrical impedance analysis. Fetal kidney structure was assessed by ultrasound. Renal function indicators (urinary albumin:creatinine and protein:creatinine) were measured in infants from a spot urine collection from nappies. Multiple linear regression and multi‐level mixed effects linear regression models with clustering were used to account for repeated measures of urine. 147 mother–child pairs were examined. Estimated fetal weight (EFW), but not fetal kidney size, was positively associated with maternal adiposity and pre‐pregnancy BMI. When adjusted for smoking, combined kidney volume relative to EFW was negatively associated with maternal percentage body fat. Infant kidney function was not influenced by maternal adiposity and pre‐pregnancy BMI (n = 84 observations). Current findings show that Indigenous babies born to obese mothers have reduced kidney size relative to EFW. We suggest that these babies are experiencing a degree of glomerular hyperfiltration in utero, and therefore are at risk of developing CKD in later life, especially if their propensity for obesity is maintained. Although no impact on renal function was observed at <2.5 years of age, long‐term follow‐up of offspring is required to evaluate potential later life impacts.