1. Monitoring programmes serve to track changes in the distribution and abundance of species. A major problem with most monitoring programmes is that species detection is imperfect and some populations are inevitably missed. Estimates of abundance and distribution are biased when detection probabilities are not taken into account.
2. Data were analysed from a large‐scale volunteer‐based amphibian monitoring programme using recently developed methods for estimating site occupancy. The analysis revealed that detection probabilities were much smaller than 100%, and varied among species and between years in an unpredictable way despite the fact that standardized field methods were used. Different environmental covariates best explained variation in detection probabilities among species and between years. It is therefore very difficult to standardize field methods in a way that eliminates such variation.
3. When detection probabilities were not taken into account, estimates of the proportion of sites where a species occurred and estimates of trends in site occupancy were biased. Bias was large and was related to detection probability.
4. Site occupancy models are a useful tool for monitoring the distribution of amphibians (and other animals and plants). These methods should be useful for assessing ‘favourable conservation status’ as required under the European Habitats Directive.