Fluid overload and prolonged mechanical ventilation lead to worse outcomes in critically ill children. However, the association between these variables in children following congenital heart surgery is unknown. The objectives of this study were to describe the association between fluid overload and duration of mechanical ventilation, oxygen requirement and radiologic findings of pulmonary and chest wall edema. This study is a retrospective chart review of patients who underwent congenital heart surgery between June 2010 and December 2013. Univariate and multivariate associations between maximum cumulative fluid balance and length of mechanical ventilation and OI were tested using the Spearman correlation test and multiple linear regression models, respectively. There were 85 eligible patients. Maximum cumulative fluid balance was associated with duration of mechanical ventilation (adjusted analysis beta coefficient = 0.53, CI 0.38–0.66, P < 0.001), length of stay in the pediatric intensive care unit (Spearman’s correlation = 0.45, P < 0.001), and presence of chest wall edema and pleural effusions on chest radiograph (Mann–Whitney test, P = 0.003). Amount of red blood cells transfused and use of nitric oxide were independently associated with increased duration of mechanical ventilation (P = 0.012 and 0.014, respectively). Fluid overload is associated with prolonged duration of mechanical ventilation and PICU length of stay after congenital heart surgery. Fluid overload was also associated with physiological markers of respiratory restriction. A randomized controlled trial of a restrictive versus liberal fluid replacement strategy is necessary in this patient population, but in the meantime, accumulating observational evidence suggests that cautious use of fluid in the postoperative care may be warranted.