This dataset provides the data underlying the manuscript Quantifying biostabilisation effects of biofilm-secreted and extracted extracellular polymeric substances (EPS) on sandy substrate published in Earth Surface Dynamics - an interactive open-access journal of the European Geosciences Union. The work was conducted in the Total Environment Simulator at the University of Hull as part of Task 9.3 of the Hydralab+ inititiative. Microbial assemblages ('biofilms') preferentially develop at water-sediment interfaces and are known to have a considerable influence on sediment stability and erodibility. There is potential for significant impacts on sediment transport and morphodynamics and, hence, on the longer-term evolution of coastal and fluvial environments. However, the biostabilisation effects remain poorly understood and quantified due to the inherent complexity of biofilms and the large spatial and temporal (i.e. seasonality) variations involved. Here, we use controlled laboratory tests to systematically quantify the effects of natural biofilm colonisation as well as extracted extracellular polymeric substances (EPS) on sediment stability. Extracted EPS may be useful to simulate biofilm-mediated biostabilisation, and potentially provides a method of speeding up time scales of physical modelling experiments investigating biostabilisation effects. We find a mean biostabilisation effect due to natural biofilm colonisation and development of almost four times that of the uncolonised sand. The presented cumulative probability distribution of measured critical threshold for erosion of colonised sand reflects the large spatial and temporal variations generally seen in natural biostabilised environments. For identical sand, engineered sediment stability from the addition of extracted EPS compares well across the measured range of the critical threshold for erosion and behaves in a linear and predictable fashion. Yet, the effectiveness of extracted EPS to stabilise sediment is sensitive to the preparation procedure, time after application and environmental conditions such as salinity, pH and temperature. These findings are expected to improve bio-physical experimental models in fluvial and coastal environments and provide much-needed quantification of biostabilisation to improve predictions of sediment dynamics in aquatic ecosystems.