Background: Cardiovascular risk in chronic kidney disease (CKD) remains high despite frequently normal conventional lipid parameters. The extent to which lipid patterns vary across CKD severity and metabolic complications remains incompletely characterized. Therefore, this study evaluated lipid patterns and their associations with renal function and CKD-related metabolic complications. Methods: This retrospective cross-sectional study included 229 CKD patients from the nephrology clinic at King Saud Medical City. Single-time-point laboratory data and clinical variables were extracted from medical records. Patients were stratified by KDIGO eGFR stage, uremia, and phosphate status. Lipid parameters were analyzed using nonparametric tests, multivariable regression, and ROC analysis. Results: Among 229 CKD patients, the most prevalent lipid abnormalities were low HDL-C (49.8%) and elevated remnant cholesterol (RC) (31.4%). HDL-C was reduced and RC increased with declining eGFR, while TC, LDL-C, and TG remained unchanged. In uremia, HDL-C remained reduced and RC increased, with additional reductions in TC and LDL-C, whereas TG did not differ. No significant lipid changes were observed with hyperphosphatemia. In multivariable analyses, HDL-C was positively associated with eGFR (β = 48.8, q = 0.003) and inversely associated with BUN (β = −14.3, q = 0.0014), while RC showed an inverse association with eGFR (β = −19.9, q = 0.0005) and a positive association with BUN (β = 3.37, q = 0.0315). These relationships remained independent of age, sex, BMI, smoking status, hypertension, and type 2 diabetes. ROC analysis further demonstrated the moderate discriminatory ability of HDL-C and RC for identifying CKD stages and uremia. Conclusions: Alterations in HDL-C and RC were independently associated with renal function and uremic status. These findings suggest that lipoprotein composition may reflect metabolic disturbances accompanying CKD progression.