Regular surveys of waterbird colonies are needed to identify changes in abundance and distribution. Consistent surveys have been maintained in some regions, but one area where updated surveys were needed was southern Manitoba, where Lakes Winnipeg, Winnipegosis and Manitoba had not been jointly surveyed since 1979. In mid-June, 2012, an aerial survey of the region was conducted using digital photography to estimate abundance of six colonial waterbird species that are regular breeders on these lakes. Breeding by at least one of the six species was confirmed at 131 locations. Double-crested Cormorant (Phalacrocorax auritus) was the most abundant breeder (43,388 pairs, 47 colonies), followed by Ring-billed Gull (Larus delawarensis, 41,819 pairs, 67 colonies), American White Pelican (Pelecanus erythrorhynchos, 12,680 pairs, 20 colonies), Common Tern (Sterna hirundo, 7,950 pairs, 31 colonies), Herring Gull (L. argentatus, 4,013 pairs, 90 colonies) and Caspian Tern (Hydroprogne caspia, 3,207 pairs, 14 colonies). Comparisons with earlier surveys in this region suggest that all six species have increased in abundance from the 1970s when populations were still recovering from earlier threats. However, Double-crested Cormorants, Caspian Terns and Common Terns show evidence of declines since the early 1990s. Standardized surveys of colonial waterbirds on these lakes should be maintained at 10-year intervals similar to the Great Lakes Monitoring Program.