The saprobic index is only regarded as a valid estimate if the sum of the abundance classes is at least 20. For example, if a survey only found a total of 500 individuals of any species, the sample would still be valid if the survey found four species with 125 individuals each (abundance class 5).
Likewise, a single water body has to be surveyed several times in different months in order to account for fluctuations.
During its history, several correcting factors have been introduced. For example, they deal with the flow rate of the river (fast-flowing water bodies are inherently better oxygenated, thus speeding up organic matter degradation), water acidification, and human-made changes to the water body. Likewise, corrections must be applied for the altitude of the ecosystem (lowland rivers naturally carry more organic matter than mountainous ones, where biomass production is lower), and for the different size of catchment areas.
The saprobic system was never designed to accurately indicate water quality if only a selection of organisms is surveyed. Deviations can be sizeable if a survey only studies ciliates and members of the macrozoobenthos (benthos animals larger than 1 millimeter), as the latter's abundance can be easily influenced by oxygen levels and not by the availability of organic matter.