* Reliance on accurate species identification - When using visual identification in the field, there is the potential for species to be misidentified, which could lead to incorrect analysis and conclusions. To reduce the likelihood of such errors, many monitoring organisations utilise laboratory verification of sample specimens for quality control purposes.
* Species specific - It can be difficult to draw comparisons between results unless the same indicator organism has been used in each study, as every species has an individual niche and associated ideal conditions. Even similar species (as defined by either taxonomy or niche) may have different reactions and different thresholds for change.
* External influences - Changes in population size or health caused by external factors may be incorrectly interpreted as resulting from changes in the environment. For example, a reduction in population that occurs due to disease, but coincides with a change in environmental conditions, could be misconstrued as resulting from the latter change.
* Misleading results - Survival of species usually regarded as sensitive can lead to the conclusion that there has been little change or contamination of an environment, which may be incorrect. An example of this is amphibians, which have traditionally been considered a highly sensitive class in regards to environmental changes, however, some research indicates that this may only be true for phenols, with amphibians having similar sensitivity to other contaminants (e.g. heavy metals) as other aquatic taxonomic groups, such as bivalves.