The immediate environment of benthic algae is reconsidered in terms of the substratum and the effect this can have on algal distribution, with particular reference to two freshwater ecosystems. Individual species often exhibit marked preferences for particular substrata, such that their presence in the littoral zone of lake systems reflects the type of substratum at different sites, while in a stream system the dynamic interaction between sediment and current velocity determines the substratum distribution and hence, to a large extent, diatom occurrence. In addition to physical differences between sediments, due to grain size, surface features etc., variation in chemical properties also potentially increases the range of contrasting niches for algal colonisation. Thus, different associations can develop within a single water body when contrasting substrata are available, although modifications in methodology may be required to recognise the finer scale patterns. Furthermore, the existence of precise species‐substratum relationships must be taken into account when benthic communities are assessed, particularly in any monitoring or predictive context, e.g. assessment of water‐quality, palaeolimnology etc.