Nanoscale secondary ion mass spectrometry (NanoSIMS) is a state-of-the-art analytical technique allowing for the visualization of the distribution of up to seven isotopes in environmental samples at high lateral resolution. The use of this technique combined with stable isotope labeling and other microscale methods will advance our understanding of biochemical cycles. Particularly, NanoSIMS has a high potential to generate new knowledge concerning functioning of microbial communities and biogeochemical interfaces because it allows for studying biogeochemical processes at the relevant scales, where they occur. In this chapter, we present this technique and its limitations and applications in recent biogeochemical research. Moreover, we show through some examples of significant advances achieved by the use of NanoSIMS how this may lead to changing paradigms in environmental sciences.