Ballast water is a dominant mechanism for the interoceanic and transoceanic dispersal of aquatic non-native species (ANS), but few studies have addressed ANS transfers via smaller scale vessel movements. We analyzed ballast water reporting records and ANS occurrence data from four US West Coast port systems to examine patterns of intra-coastal ballast water transfer, and assess how ballast transfers may have influenced the secondary spread of ANS. In 2005, one third of the vessels arriving to the US West Coast originated at one of four West Coast port systems (intra-coastal traffic). These vessels transported and discharged 27% (5,987,588 MT) of the total ballast water volume discharged at these ports that year. The overlap of ANS (shared species) among port systems varied between 3% and 80%, with the largest overlap occurring between San Francisco Bay and LA/Long Beach. Our results suggest that intra-coastal ballast water needs further consideration as an invasion pathway, especially as efforts to promote short-sea shipping are being developed.