Biodiversity conservation cannot operate in Central Eastern European countries without a well-established monitoring system, that is dependent on the citizen scientists input. Here we analyse, based on a Polish case: (1) The contribution of NGOs to the national nature monitoring scheme and their collaboration with governmental and scientific institutions and (2) the motivation of citizen scientists to volunteer for NGOs’ monitoring activities. The study comprises a focus group interview, 30 in-depth interviews with coordinators, citizen scientists, experts and a 23 days long participant observation of a model NGO. We have assessed the monitoring input of NGOs as being a contributory factor influencing the biodiversity conservation effectiveness. The cooperation between governmental, scientific institutions and NGOs exists, but is dependent on national funding. Although NGOs highlight the lack of coherence in monitoring methodology, they are willing to join the biodiversity monitoring, especially at the European Ecological Network – Natura 2000 sites. On the other hand the trust concerning cooperation with citizen scientists is limited. However, despite this, they still turned out to be trustworthy partners. The most effective way to maintain cooperation with citizen scientists is to create a bond in a group and to provide them with the opportunity to develop their passion for nature. Our findings have shed light on the growing importance of citizen scientists in biodiversity governance, providing recommendations for development of the effective monitoring schemes based on the volunteer work of citizen scientists.