Abstract The time-varying reproduction number (Rt: the average number secondary infections caused by each infected person) may be used to assess changes in transmission potential during an epidemic. While new infections are not usually observed directly, they can be estimated from data. However, data may be delayed and potentially biased. We investigated the sensitivity of Rt estimates to different data sources representing Covid-19 in England, and we explored how this sensitivity could track epidemic dynamics in population sub-groups. We sourced public data on test-positive cases, hospital admissions, and deaths with confirmed Covid-19 in seven regions of England over March through August 2020. We estimated Rt using a model that mapped unobserved infections to each data source. We then compared differences in Rt with the demographic and social context of surveillance data over time. Our estimates of transmission potential varied for each data source, with the relative inconsistency of estimates varying across regions and over time. Rt estimates based on hospital admissions and deaths were more spatio-temporally synchronous than when compared to estimates from all test-positives. We found these differences may be linked to biased representations of subpopulations in each data source. These included spatially clustered testing, and where outbreaks in hospitals, care homes, and young age groups reflected the link between age and severity of disease. We highlight that policy makers could better target interventions by considering the source populations of Rt estimates. Further work should clarify the best way to combine and interpret Rt estimates from different data sources based on the desired use.