The purpose of this study was to evaluate the hemodynamic properties and microemboli capture associated with different vacuum‐assisted venous drainage (VAVD) vacuum levels and venous reservoir levels in a neonatal cardiopulmonary bypass circuit. Trials were conducted in 2 parallel circuits to compare the performance of Capiox Baby RX05 oxygenator with separate AF02 arterial filter to Capiox FX05 oxygenator with integrated arterial filter. Arterial cannula flow rate to the patient was held at 500 mL/min and temperature maintained at 32°C, while VAVD vacuum levels (0 mm Hg, −15 mm Hg, −30 mm Hg, −45 mm Hg, −60 mm Hg) and venous reservoir levels (50 mL, 200 mL) were evaluated in both oxygenators. Hemodynamic parameters measuring flow, pressure, and total hemodynamic energy were made in real time using a custom‐made data acquisition system and Labview software. Nearly 10 cc bolus of air was injected into the venous line and gaseous microemboli detected using an Emboli Detection and Classification Quantifier. Diverted blood flow via the arterial filter’s purge line and mean pressures increased with increasing VAVD levels (P < 0.01). Mean pressures were lower with lower venous reservoir levels and were greater in RX05 groups compared to FX05 (P < 0.01). Microemboli detected at the preoxygenator site increased with higher VAVD vacuum levels and lower venous reservoir levels (P < 0.01). The amount of microemboli captured by the FX05 oxygenator with integrated arterial filter was greater than by the RX05 oxygenator alone, although both oxygenators were able to clear microemboli before reaching the pseudo‐patient.