This study defines criteria for the use of benthic foraminifera (protists) as a quick and efficient bio-monitoring tool to implement marine legislation. Various sampling and preparation procedures are investigated in an attempt to find the optimal methodology for environmental monitoring using soft-sediment foraminifera with the objective of assessing ecological quality status (EcoQS). Twenty-seven sampling stations in silled basins along the Norwegian Skagerrak coast, NE North Sea, are investigated for environmental parameters and living (stained, including soft-shelled forms) and dead benthic foraminifera. Diversity, expressed as the effective number of species (exp H′bc) and community composition are used to evaluate EcoQS using living (stained) benthic foraminifera. Correlation studies show that bottom-water dissolved oxygen concentration at the time of sampling ([O2]tos) is the main environmental factor controlling variation in diversity. Variables such as grain size, C/N, TOC and TN are less important. Correlation between foraminiferal diversity and [O2]tos, as well as correlation between community data and [O2]tos, suggest that benthic foraminifera represent an efficient bio-monitoring tool to evaluate EcoQS. A clear pattern from “bad” to “high” EcoQS is established using the strong link between the benthic foraminiferal diversity and the bottom-water oxygen gradient. The study shows that EcoQS can be evaluated quickly and accurately using the following method: sample the top 1 cm of sediment, dry-pick about 250 living (stained) individuals of >125 μm-sized fossilisable (i.e. most of those remaining subsequent to drying) foraminifera from each of three replicates. exp(H′bc) based on living benthic foraminifera is a promising tool to assess EcoQS. For fossil assemblages, exp(H′bc) has potential for evaluating temporal changes in in situ PaleoEcoQS and for defining reference conditions from pre-impacted times.