The combination of an acid-inducing diet and reduced nephron mass is associated with a progressive decline in glomerular filtration rate (GFR) that can be corrected by dietary alkali. Here we determined whether the higher tissue acid content mediates the decline in GFR. Using Munich-Wistar rats we induced sub-total nephrectomy and measured by microdialysis the tissue acid content in the kidney cortex and in the paraspinous muscle. The GFR was lower in the rats with reduced nephron mass at 1 and 13 weeks following subtotal nephrectomy compared to the sham-operated rats. Both groups of rats ate the same acid-inducing casein-based diet and had similar plasma acid-base parameters and net urine acid excretion. However, rats with reduced nephron mass had higher tissue acid content compared to control animals and had a lower GFR at week 13 compared to that measured at week 1. Adding dietary acid to the casein diet led to an even higher tissue acid and lower GFR by week 13. By contrast, adding alkali to the casein diet or placing animals with reduced nephron mass on a soy-based diet led to a lower tissue acid content and no decline in GFR. Animals with reduced nephron mass on a soy-based diet given dietary acid had a higher tissue acid content and a decline in GFR. These studies show that dietary maneuvers that increase the tissue acid content reduce GFR, whereas diets that lower the tissue acid level preserve GFR during chronic kidney failure.