Intertidal and transitional waters, situated at the interface between marine and terrestrial ecosystems, are under the influence of both marine and fresh water inputs. These ecotones are some of the most productive ecosystems globally. Representing at least 13% of the world’s coastline, they provide human societies with a range of ecosystem goods and services. To protect and restore these fragile ecosystems, many nations have enacted marine legislations. The implementation of these legislations worldwide is generating a fruitful debate amongst marine scientists about how to define and implement efficient and reliable bio-assessment tools. A component of the meiofauna, benthic foraminifera (protists), has been widely used as bio-indicators of several pollution sources in coastal and transitional waters. In this work, I will synthetize studies we conducted with the aim (i) to develop the use of benthic foraminifera as indicator of the health of benthic habitats, (ii) to characterize the motion-behavior of benthic foraminifera and possible application of this group as a bioassay and (iii) to understand the function of benthic foraminifera in bioturbation processes. In details, our works confirmed that foraminifera can be considered as a reliable biological quality element to assess the ecological quality status in transitional and marine systems. Specifically, the use of the diversity index exp(H’bc) based on benthic foraminifera showed good performance in detecting the impact of pollution in different contexts. This method was originally tested along a decreasing gradient of bottom-water oxygen concentration in SE Norwegian fjords and we showed it may work against most pollution sources like aquaculture, dike construction and heavy metals. Furthermore, our effort to assign foraminiferal species to ecological groups of sensitivity to total organic carbon showed that the classification reflects differences in species tolerance of organic load-related stress. We then obtained good evaluation of the ecological quality status with the use of the sensitivity-based Foram-AMBI index. Our experiments on the motion-behavior showed that benthic foraminifera displayed a high variability in their travelled distance but also in their motion behavior, e.g. tortuosity, vertical position; exhibiting typical responses of stressed organisms. Last, we reported that despite their minute size benthic foraminifera may play a significant role, though still largely overlooked, in intertidal mudflats sediment reworking. In details, bioturbation by benthic foraminifera is the result of the complex interplay between species-specific features such as motion behavior, phenotypic plasticity and functional classification, i.e. bioturbation mode. In conclusion, we believe that benthic foraminifera offer a putatively endless sets of opportunities to tackle the question of the potential effects of new global stressors, from the physiological to the ecosystem level. We plea here to embrace the opportunity to see in these minute organisms a unique prospect to refine our understanding of the effects of the new environmental threats of the “Anthropocene” on the structure and functions at play behind the future of transitional and intertidal ecosystems under climate change.