Abstract Citizen science has great potential to foster ecological knowledge, skills and collective action for biodiversity conservation. To date, however, there are few experimental studies of behaviour change outcomes induced by citizen science. We assessed the effects of citizen science in ecological stream monitoring on participants' individual and collective behaviour and action intentions to protect streams beyond the immediate scope of the citizen science project. For this we applied a three‐wave, quasi‐experimental survey design with a citizen science treatment group (N = 213 participants of the project FLOW in Germany) and two control groups (waiting control group: N = 92, panel control group: N = 250). In addition, we analysed citizen science effects on potential predictors of freshwater conservation behaviour, such as knowledge, skills, awareness of stream stressors and group identification. Results of linear mixed‐model analysis showed that, compared to the control groups, citizen scientists significantly increased their objective stream‐related knowledge, their self‐reported stream monitoring skills and their awareness of stream stressors. These changes remained stable 6 weeks after the citizen science intervention. Notably, citizen scientists also reported increased identification with their citizen science project group and higher levels of collective and personal behaviour to protect streams at posttest (e.g. contacting local politicians with ideas for stream protection or using biodegradable detergents). Analysis revealed that increases in group identification and collective stream protection behaviour were significantly correlated. We could show that the citizen science intervention was particularly effective for participants with high intrinsic motivation and for those with low prior knowledge and experience in stream monitoring. Synthesis and applications. Citizen science can serve as a useful tool to promote ecological understanding, awareness and collective action to conserve freshwater streams. By fostering volunteer skills and community building, citizen science projects can empower participants with different levels of experience to engage in freshwater monitoring and protection. Decision makers should actively support approaches for citizen participation in freshwater monitoring, recognising that collective engagement of diverse community members is needed to finally meet the European Water Framework Directive's goal of restoring the good ecological status of freshwater ecosystems. Read the free Plain Language Summary for this article on the Journal blog.