The rapid expansion of urban areas leads to loss, fragmentation, and degradation of natural habitats, posing a serious threat to biodiversity. While urban ponds might contribute substantially to the biodiversity of urban blue-green infrastructure, the role of garden ponds, one of their most numerous representatives, is still little known. We lack a comprehensive understanding of how local habitat features, different forms of management, and urbanisation might impact the biodiversity of these habitats. This study aimed to reveal the importance of garden ponds via a country-wide online citizen science survey in Hungary, Central Europe. Based on data from over 800 pond owners, we gained knowledge about the prevalence and local frequency of various native animal groups, including amphibians, odonates, and birds, as well as information regarding introduced animals, such as fish. Additionally, we collected data about pond features and management practices. We tested the effect of pond features, pond management, and landscape-level drivers (urbanisation, surrounding wetland coverage) on the presence of conspicuous animal groups (adult amphibians, birds, odonates, and tadpoles) along with species of adult amphibians to identify the potential drivers of the biodiversity of garden ponds. Key pond features like pond age, area, aquatic and shoreline vegetation were the most important factors, while algaecide addition was the most influential management practice negatively affecting the presence of amphibians. Urbanisation had a negative effect on the presence of adult amphibians and their tadpoles, but surprisingly, it was not negatively associated with the presence of odonates and birds. Our results demonstrate the vital role of garden ponds in urban biodiversity conservation, most notably by providing secondary habitats and contributing to amphibian conservation, as evidenced by the occurrence of 13 species. Emphasizing public involvement is key in developing effective urban biodiversity conservation strategies and recognizing citizens’ potential contributions to a better functioning blue-green infrastructure.Graphical abstractGraphical abstract:Summary of the key results from the MyPond survey. Arrows indicate significant relationships (blue: positive, red: negative) between the presence of animal groups and pond features and management practices)HighlightsOver 800 garden pond owners participated in a citizen science project in Hungary.Garden ponds can host flagship animal groups, e.g., amphibians, odonates, and birds.Pond age, area, and vegetation influenced the occurrence of these animal groups.Urbanisation had a negative effect on amphibian communities.Algaecide application played a key role in the presence of multiple animal groups.