All organs atrophy if you increase their pressures due to relative ischemia ( Reduced perfusion pressure ) . If its acute (e.g Toxic megacolon/Appendicitis ) you get necrosis and the organ gets $$$$ed up .. If its subacute ( pancreatic duct obstruction / nephrolithiasis / etc.. ) you get a mix of apoptosis/shrinking of cells --> Grossly looks like atrophy and the organ works sub optimally , or eventually , it doesn't work at all . Specifically in the kidney its like Pax Roma said , the cortex gets squeezed so it atrophies --> Glomeruli don't work , but the ducts/pelvis is filled up with urine , so it looks distended/big