Many countries have adopted a single, well-described approach to the use of phototrophs for monitoring river water quality, which involves the use of indices related to diatom composition at a site. Increasingly these indices have focussed on assessing ambient phosphate concentration. However, there is a wide range of other methods which can provide additional information to make up for any weaknesses in the standard method. Some of these methods are reviewed briefly here. They can be useful, for instance, when considering temporal and spatial variability in phosphate concentration at a particular site and providing much more insight on heavy metal or pesticide pollution than revealed by routine water analysis.