The relationship between increased cerebral spinal fluid (CSF) ventricular compartments, structural and microstructural dysmaturation, and executive function in patients with congenital heart disease (CHD) is unknown. Here, we leverage a novel machine-learning data-driven technique to delineate interrelationships between CSF ventricular volume, structural and microstructural alterations, clinical risk factors, and sub-domains of executive dysfunction in adolescent CHD patients. We trained random forest regression models to predict measures of executive function (EF) from the NIH Toolbox, the Delis-Kaplan Executive Function System (D-KEFS), and the Behavior Rating Inventory of Executive Function (BRIEF) and across three subdomains of EF - mental flexibility, working memory, and inhibition. We estimated the best parameters for the random forest algorithm via a randomized grid search of parameters using 10-fold cross-validation on the training set only. The best parameters were then used to fit the model on the full training set and validated on the test set. Algorithm performance was measured using root-mean squared-error (RMSE). As predictors, we included patient clinical variables, perioperative clinical measures, microstructural white matter (diffusion tensor imaging- DTI), and structural volumes (volumetric magnetic resonance imaging- MRI). Structural white matter was measured using along-tract diffusivity measures of 13 inter-hemispheric and cortico-association fibers. Structural volumes were measured using FreeSurfer and manual segmentation of key structures. Variable importance was measured by the average Gini-impurity of each feature across all decision trees in which that feature is present in the model, and functional ontology mapping (FOM) was used to measure the degree of overlap in feature importance for each EF subdomain and across subdomains. We found that CSF structural properties (including increased lateral ventricular volume and reduced choroid plexus volumes) in conjunction with proximate cortical projection and paralimbic-related association white matter tracts that straddle the lateral ventricles and distal paralimbic-related subcortical structures (basal ganglia, hippocampus, cerebellum) are predictive of two-specific subdomains of executive dysfunction in CHD patients: cognitive flexibility and inhibition. These findings in conjunction with combined RF models that incorporated clinical risk factors, highlighted important clinical risk factors, including the presence of microbleeds, altered vessel volume, and delayed PDA closure, suggesting that CSF-interstitial fluid clearance, vascular pulsatility, and glymphatic microfluid dynamics may be pathways that are impaired in CHD, providing mechanistic information about the relationship between CSF and executive dysfunction.