A growing body of evidence suggests that chronic, sport-related head impact exposure can impair brain functional integration and brain structure and function. Evidence of a robust inverse relationship between the frequency and magnitude of repeated head impacts and disturbed brain network function is needed to strengthen an argument for causality. In pursuing such a relationship, we used cap-worn inertial sensors to measure the frequency and magnitude of head impacts sustained by eighteen intercollegiate water polo athletes monitored over a single season of play. Participants were evaluated before and after the season using computerized cognitive tests of inhibitory control and resting electroencephalography. Greater head impact exposure was associated with increased phase synchrony [r (16) > 0.626, p < 0.03 corrected], global efficiency [r (16) > 0.601, p < 0.04 corrected], and mean clustering coefficient [r (16) > 0.625, p < 0.03 corrected] in the functional networks formed by slow-wave (delta, theta) oscillations. Head impact exposure was not associated with changes in performance on the inhibitory control tasks. However, those with the greatest impact exposure showed an association between changes in resting-state connectivity and a dissociation between performance on the tasks after the season [r (16) = 0.481, p = 0.043] that could also be attributed to increased slow-wave synchrony [F (4, 135) = 113.546, p < 0.001]. Collectively, our results suggest that athletes sustaining the greatest head impact exposure exhibited changes in whole-brain functional connectivity that were associated with altered information processing and inhibitory control.