Vibrational spectroscopy offers ecologists the opportunity to perform sensitive and non-destructive analyses, rapidly. The main purpose of this chapter is to illustrate some of many emerging applications of vibrational spectroscopy in the field of diagnosis and screening of aquatic environments. The sections of this chapter will summarize many innovative studies utilizing vibrational spectroscopy in order to answer ecologically based questions on aquatic species. The advantages of this technique will be presented thoroughly by revealing the diversity of aquatic species investigated with this tool. This summary of the work done in the field will benefit aquatic ecologists trying to go beyond their boundaries.