Rising rates of metabolic syndrome, obesity, and mortality from chronic kidney disease (CKD) have prompted further investigation into the association between metabolic phenotypes and CKD. Purpose: To report the frequency of strictly defined metabolic phenotypes, renal function within each phenotype, and individual risk factors associated with reduced renal function. We utilized the 2013–2018 National Health and Nutrition Examination Surveys (NHANES) and complex survey sample weighting techniques to represent 220 million non-institutionalized U.S. civilians. Metabolic health was defined as having zero of the risk factors defined by the National Cholesterol Education Program with the exception of obesity, which was defined as BMI ≥ 30 kg/m2 in non-Asians and BMI ≥ 25 kg/m2 in Asians. The metabolically healthy normal (MUN) phenotype comprised the highest proportion of the population (38.40%), whereas the metabolically healthy obese (MHO) was the smallest (5.59%). Compared to the MHN reference group, renal function was lowest in the strictly defined MUN (B = −9.60, p < 0.001) and highest in the MHO (B = 2.50, p > 0.05), and this persisted when an increased number of risk factors were used to define metabolic syndrome. Systolic blood pressure had the strongest correlation with overall eGFR (r = −0.25, p < 0.001), and individuals with low HDL had higher renal function compared to the overall sample. The MUN phenotype had the greatest association with poor renal function. While the MHO had higher renal function, this may be due to a transient state caused by renal hyperfiltration. Further research should be done to investigate the association between dyslipidemia and CKD.