Future anthropogenic warming is suggested to have major impacts on global biodiversity, with freshwater ecosystems particularly under threat. Understanding the role of temperature in impacting freshwater biodiversity is therefore of paramount importance. Previous research suggested that temperature has a limited influence on freshwater diversity across the Holocene. However, this is mostly based on data resolved at centennial to millennial scales, and it is therefore unknown whether freshwater diversity responds similarly over shorter (decadal/multi-decadal) timescales. We present aquatic insect (Chironomidae) summer temperature reconstructions and key diversity metrics (α-diversity, β-diversity, and network skewness) from three annually laminated lacustrine records from Europe (Diss Mere, UK; Nautajärvi, Finland; and Meerfelder Maar, Germany) across the Holocene, including multi-decadal resolutions within the Holocene Thermal Maximum (HTM) to test this. Our results reveal three major findings with both spatial and temporal elements: (1) At regional (European) scales, using all available data, there is a significant decline in all three diversity metrics with increased summer temperature; (2) at local multi-decadal scales across the HTM, in the absence of additional major land-use and eutrophication drivers, summer temperature has only a minor control on aquatic insect diversity (with the exception of a proposed cooling between 6.2 and 5.9 ka BP); and (3) at local low-frequency timescales, we find a similar relationship, albeit with warm temperatures appearing to promote assemblage stability. As such, temperature and diversity relationships are complex and non-linear through time and space. We argue that understanding variability in aquatic insect diversity across different temporal and spatial scales is important to consider when assessing the potential for future biodiversity changes under warming climatic regimes in the coming decades.