Biodiversity loss driven by anthropogenic forcing is a critical global challenge. While increasing rates in turnover within communities are widely documented, to determine if turnover equates to biodiversity loss, it needs to be interpreted with respect to concurrent changes in spatial (or ‘regional’) biodiversity. In particular, the influence of community homogenisation among ecosystems on temporal trends in biodiversity must be quantified. However, the disconnect between ecological monitoring and human impact timeframes has resulted in gaps in our ability to test for community homogenisation. Here we demonstrate that community homogenisation among ecosystems can obscure local biodiversity loss. Among six lakes in Aotearoa New Zealand, while individual lake biodiversity remained stable over 300 years of agricultural land use history, community homogenisation and loss of regional biodiversity occurred with increasing agricultural intensification. By tracking community assemblages among multiple geographically distinct ecosystems over a common impact history, this study was able to test for biotic homogenisation among ecosystems unequivocally. Our findings highlight the risk of underestimating biodiversity loss when regional dynamics are not considered and demonstrate a gap in biodiversity assessments that focus solely on within-ecosystem trends.