Diabetic kidney disease (DKD) is a leading cause of end‐stage renal disease and renal replacement therapy worldwide. A pathophysiological hallmark of DKD is glomerular basal membrane (GBM) thickening, whereas this feature is absent in minimal change disease (MCD). According to fundamental transport physiological principles, a thicker GBM will impede the diffusion of middle‐molecules such as cystatin C, potentially leading to a lower estimated GFR (eGFR) from cystatin C compared to that of creatinine. Here we test the hypothesis that thickening of the glomerular filter leads to an increased diffusion length, and lower clearance, of cystatin C. Twenty‐nine patients with a kidney biopsy diagnosis of either DKD (
n
= 17) or MCD (
n
= 12) were retrospectively included in the study. GBM thickness was measured at 20 separate locations in the biopsy specimen and plasma levels of cystatin C and creatinine were retrieved from health records. A modified two‐pore model was used to simulate the effects of a thicker GBM on glomerular water and solute transport. The mean age of the patients was 52 years, and 38% were women. The mean eGFR
cystatin C
/eGFR
creatinine
‐ratio was 74% in DKD compared to 98% in MCD (
p
< 0.001). Average GBM thickness was strongly inversely correlated to the eGFR
cystatin C
/eGFR
creatinine
‐ratio (Pearson's
r
= −0.61,
p
< 0.01). Two‐pore modeling predicted a eGFR
cystatin C
/eGFR
creatinine
‐ratio of 78% in DKD. We provide clinical and theoretical evidence suggesting that thickening of the glomerular filter, increasing the diffusion length of cystatin C, lowers the eGFR
cystatin C
/eGFR
creatinine
‐ratio in DKD.