The application of molecular techniques has revolutionized freshwater and marine ecology, especially for plankton research. Methods, such as denatured gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), and single-strand conformation polymorphism (SSCP), together with environmental clone libraries, have unraveled an unexpected biodiversity of organisms in the water column. Molecular probes are just entering the field of commercialization for monitoring toxic algal blooms. Genomics and metagenomics were recently introduced into marine biology. At the basis of all molecular approaches is the isolation of nucleic acids from cultures, tissue, or environmental samples. Here, we summarize methods, quality controls, and hints for sample treatment to reliably isolate nucleic acids, both DNA and RNA, from environmental aqueous samples. This chapter not only is directed to researchers inexperienced with such methods but also is an aid to those already working in the field. It may be used as a step-by-step guide for nucleic acid isolation from field samples, and we make suggestions for subsequent use of the DNA/RNA.