Abstract Between 2002 and 2019, monitoring of Common Tern Sterna hirundo and Little Tern Sternula albifrons along the Sava River near Zagreb, Croatia was conducted. Natura 2000 site “Sava kod Hrušćice” was designated to protect colony at river islands, with estimated population sizes of 100–150 pairs of Common and 20 pairs of the Little Tern. Flooding of the colony caused breeding failure in several years. Common Terns moved to breed on islands in gravel pits with a total population around 150 pairs, while Little Tern did not breed after 2010. In the last few years, terns have not bred at Hrušćica and the only colony inside the Natura 2000 site is situated on a breeding platform at Siromaja gravel pit. Channelling of rivers and hydropower plants are the main threats, changing natural dynamics of water level and causing reduction of gravel sediment in rivers.