Citizen science monitoring programmes are making increasingly important contributions to wildlife conservation, often at spatial and temporal scales unachievable by individual or teams of researchers. They are particularly valuable in estimating population trends and management impacts, and thus informing effective conservation decisions for declining species. The quality and potential biases of citizen science data are of concern, however, and appropriate experimental design and analysis are needed to ensure that the maximum scientific value is extracted. We investigated these issues in a citizen science survey of the Endangered Carnaby's black-cockatoo Calyptorhynchus latirostris. Since 2010, citizen scientists have conducted synchronized annual counts of Carnaby's black-cockatoo at roost sites to estimate the population trend. Survey effort was substantial, with c. 150 sites surveyed by > 260 volunteers each year. Relatively few sites were occupied, however, and only 42 (16%) of the 265 sites surveyed in total accounted for 95% of all observations. Many sites were empty and survey effort was often inconsistent. Taking these issues into account, analysis showed a statistically significant decline in roost occupancy rate and a non-significant decline in the mean size of roosting flocks, with an estimated overall trend of 14% decline per annum in the number of roosting birds. We highlight three important issues for citizen science monitoring programmes: the need to maintain regular surveys of sample sites to avoid patchy data, use an appropriate model that accounts for variable survey effort, high frequency of zero counts, and sampling site turnover, and incorporate information on site characteristics to help explain variation.