Abstract Background and Aims Megalin is an endocytic receptor located in the apical membrane of proximal tubule (PT) cells. It prevents low molecular-weight proteinuria by reuptake of a variety of proteins from the filtrate. Megalin is required for normal uptake of Cubilin-bound proteins, but it is unknown if the receptor is important for other apical PT proteins. Carbonic anhydrase 4 (CA4) is an enzyme crucial for PT bicarbonate reuptake. Our aim was to investigate the relationship between the expression patterns of these two proteins. Method A mouse model of kidney-specific mosaic megalin-knockout (M-KO). Liquid chromatography-mass spectrometry (LC-MS) on mouse kidney cortex. Immunohistochemistry (IHC), electron microscopy (EM) and Western blotting (WB) of mouse kidney. Biochemical analysis of mouse blood and urine. Results LC-MS revealed a 4.23-fold increase in CA4 abundance in M-KO mice together with smaller but also statistically significant alterations in other acid-base-associated proteins. IHC shows that the increase in CA4 abundance specifically was in the cells lacking megalin, while cells with megalin retained normal abundance. The same pattern was observed in a biopsy from a patient lacking megalin. WB revealed increased shedding of CA4 in urine from M-KO mice and EM showed mislocalization of CA4. Conclusion We show a hitherto unknown relationship where the expression and subcellular localization of CA4 is altered in PT-cells lacking megalin and show that M-KO mice have altered acid-base handling. Comparable blood parameters at baseline are maintained despite differences in urinary excretion and when challenged with acetazolamide the urinary excretion of the groups becomes alike, however blood parameters become different. While the mechanisms and full extend are unknown, this links megalin to the acid-base regulating systems of the PT.