Introduction: Nephrolithiasis is a known risk factor for chronic kidney disease (CKD); however, it is unknown how CKD affects urinary parameters related to stone risk. The purpose of this study was to assess the relationship of diminishing glomerular filtration rate (GFR) and kidney stone-related 24-hour urine (24H urine) composition. Materials and Methods: A single-institution retrospective review of patients (n = 2057) who underwent 24H urine analysis was performed. The serum creatinine within 1 year of the first 24H urine was used to determine estimated GFR and stratify patients by CKD stage. We performed analysis of variance and multivariable linear regression to assess the relationship of GFR and urinary analytes. Results: Among all patients, there were 184 (8.9%), 1537 (74.7%), 245 (11.9%), 70 (3.4%), 17 (0.8%), and 4 (0.2%) in CKD stage I, II, IIIa, IIIb, IV, and V groups, respectively. On analysis of 24H urine composition, as CKD increased, changes in urinary parameters protective against crystallization included decreased calcium and uric acid (UA) (P < 0.001). In addition, parameters favoring crystallization included decreased citrate and magnesium (P = 0.002 and P < 0.001, respectively). The net effect with increasing GFR was decreasing supersaturation of calcium oxalate and phosphate. On linear regression, urinary excretion of calcium, oxalate, citrate, UA, phosphate, and ammonia all decreased with decreasing GFR (all P < 0.05). Conclusions: Higher CKD stage was associated with changes in urinary analytes that both promoted and inhibited stone formation, with the net effect of decreasing calcium oxalate and phosphate supersaturation. These patients may benefit from medical therapy that targets improving urinary citrate instead of lowering calcium or UA.