Bioirrigation, the exchange of solutes between overlying water and sediment by benthic organisms, plays an important role in sediment biogeochemistry. Bioirrigation either is quantified based on tracer data or a community (bio)irrigation potential (IPc) can be derived based on biological traits. Both these techniques were applied in a seasonal study of bioirrigation in subtidal and intertidal habitats in a temperate estuary. The combination of a tracer time series with a high temporal resolution and a mechanistic model allowed for us to simultaneously estimate the pumping rate and the sediment attenuation, a parameter that determines irrigation depth. We show that, although the total pumping rate is similar in both intertidal and subtidal areas, there is deeper bioirrigation in intertidal areas. This is explained by higher densities of bioirrigators such as Corophium sp., Heteromastus filiformis and Arenicola marina in the intertidal, as opposed to the subtidal, areas. The IPc correlated more strongly with the attenuation coefficient than the pumping rate, which highlights that the IPc index reflects more the bioirrigation depth than the rate.