In 2022–2023, Europe experienced significant outbreaks of highly pathogenic avian influenza (HPAI) affecting both poultry and wild birds. These outbreaks had notable impacts on various bird species, especially those nesting in colonies. In the Odra estuary and its lower section, a particularly important area for gregarious waterbirds, 23 breeding colonies were examined in 2023. The total number of breeding pairs (bp) was 12,439. No symptoms of HPAI were found in Cormorants Phalacrocorax carbo (8,899 bp), Grey Herons Ardea cinerea (503 bp) and Pied Avocet Recurvirostra avosetta (25 bp). HPAI symptoms were found among colonies of gulls and terns, primarily in Black-headed Gull Chroicocephalus ridibundus (BHG) (2,484 bp, 14% mortality rate) and in Common Tern Sterna hirundo (CT) (656 bp, 12% mortality rate). Among the colonies of terns of the genus Chlidonias, low mortality was observed — 1 adult individual (143 bp of Black Tern Chlidonias niger, 0.2% mortality rate) and no dead individuals among Whiskered Tern Chlidonias hybrida. All samples taken from the BHG and CT (N = 20) from affected colonies contained genetic material of avian influenza A. Lower bird density in the colony results in lower mortality. Additionally, a larger area of suitable breeding habitat reduces bird mortality. There was no significant difference in mortality between artificial and natural habitats. The lowest mortality was in natural habitats with floating vegetation. There was higher mortality on natural islands compared to artificial ones. The highest mortality occurred in colonies dominated by BHG and CT. Small artificial floating platforms may contribute to episodes of mass mortality in epidemic conditions due to high density and easy virus spread. Large artificial islands may be safer, a density of 3 bp/100 m², the mortality rate was 1.1%, while on small artificial platforms with an average density of 92 bp/100 m², the mortality rate was 25%.