Direct observations on chemical micro-environment and microbial composition in biofilms are rare. The combination of microsensor and molecular techniques is highly useful for studies on the microbial ecology of biofilms. We shortly describe some applications of microsensors to study mass transfer phenomena and microbial processes in biofilms. It has recent been recognized that biofilms are not always flat layers of cells, but can consist of complex structures allowing liquid flow. Thus the classical view, that transport in biofilms is diffusional, is challenged. In laboratory grown biofilms the effect of convection on mass transfer was demonstrated. The microsensor technique has improved, so that direct in situ measurements in living biofilms are possible. By direct measurements of liquid flow with microsensors we show that in biofilms grown in bioreactors heterogeneity and convectional transport must also be taken into account. For the description of the microbial population we use molecular techniques, such as in situ hybridisation with 16S rRNA-targeted oligonucleotide probes. In a nitrifying-denitrifying biofilm we found a complex nitrifying community consisting of members of the genera Nitrosomonas, Nitrosospira, Nitrobacter and Nitrospira. Their occurrence was correlated with nitrification activity as determined by microsensor measurements.