Small rivers support high levels of biodiversity, being especially sensitive to the effects of global change. Temporal records of community composition in minimally impaired streams can be used to explore trends in biodiversity in response to climate change and natural temporal variation. We approached the comparison of two time periods (2003–2008 and 2016–2020) to study whether the composition of diatom assemblages changed over time in twenty-three streams of the mountain range of Picos de Europa (Northern Spain). The stream’s water chemistry indicated significant decreases in N_NO3− and P_PO43− content over time. In these minimally disturbed streams, the specific diatom community was dominated by Achnanthidium pyrenaicum, Achnanthidium minutissimum and Cocconeis euglypta. PERMANOVA analyses did not identify significant changes in diatom assemblage composition between periods or river types. Diatom indices (e.g. IPS, NORTIdiat) indicated high or good ecological status and relatively high alpha diversity values were found in these mountain rivers during the studied years. Although diversity and evenness showed a significant decrease over time, the temporal stability of the river-type diatom reference community between the two periods should be considered as an indicator of biodiversity persistence of high importance when monitoring the ecological status following the reference condition approach.