Almost straight after the break Owen Garvan doubled Town's lead following a mistake by the home keeper, before adding his second and Town's third just after the hour mark.
Connor Wickham also had the ball in Waterford's net in the closing stages, but like fellow young striker Rhodes in the first half, Town's youngest ever First Team player had his goal ruled out for offside.
Town Side: R.Wright, Bruce, McAuley, Balkestein, O'Connor (Smith 46), Norris (Trotter 46), Shumulikoski, Garvan, Quinn, Lisbie (Stead 62), Rhodes (Wickham 62).