Type II nephronophthisis (NPHP2) is an autosomal recessive renal cystic disorder characterized by mutations in the inversin gene. Humans and mice with mutations in inversin have enlarged cystic kidneys that may be due to fluid accumulation resulting from altered ion transport. To address this, transepithelial ion transport was measured in shRNA mediated inversin-depleted mouse cortical collecting duct (mCCD) cells. Loss of inversin decreased the basal ion flux in mCCD cells compared to controls. Depletion of inversin decreased vasopressin-induced Na+ absorption, but did not alter Cl- secretion by mCCD cells. Addition of amiloride, a specific blocker of the epithelial sodium channel (ENaC), abolished basal ion transport in both inversin knockdown and control cells indicating ENaC involvement. Transcript levels of ENaCβ subunit were reduced in inversin-knockdown cells consistent with decreased ENaC activity. Furthermore, Nedd4l (neural precursor cell expressed, developmentally downregulated 4 like), an upstream negative regulator of ENaC was evaluated. The relative amount of the phosphorylated, inactive Nedd4l was decreased in inversin-depleted cells consistent with decreased ENaC activity. The protein levels of Sgk1 (serum and glucocorticoid-inducible kinase) that phosphorylates Nedd4l remain unchanged although the transcript levels were increased in inversin-depleted cells. Interestingly, mRNA and protein levels of Crtc2 (Creb-regulated transcription coactivator) kinase, a positive regulator of Sgk1 were decreased in inversin-depleted cells. Together these results suggest that loss of inversin decreases Na+ transport via ENaC, mediated in part by transcriptional and post-translational regulation of Crtc2/Sgk1/Nedd4l axis as a contributory mechanism for enlarged kidneys in NPHP2.