Increased frequency and extent of potentially harmful blooms in coastal and inland waters world-wide require the development of methods for operative and reliable monitoring of the blooms over vast coastal areas and a large number of lakes. Remote sensing could provide the tool. An overview of the literature in this field suggests that operative monitoring of the extent of some types of blooms (i.e. cyanobacteria) is relatively straightforward. Operative monitoring of inland waters is currently limited to larger lakes or using airborne and hand-held remote sensing instruments as there are no satellite sensors with sufficient spatial resolution to provide daily coverage. Extremely high spatial and vertical variability in biomass during blooms of some phytoplankton species and the strong effects of this on the remote sensing signal suggest that water sampling techniques and strategies have to be redesigned for highly stratified bloom conditions, especially if the samples are collected for algorithm development and validation of remote sensing data. Comparing spectral signatures of different bloom-forming species with the spectral resolution available in most satellites and taking into account variability in optical properties of different water bodies suggests that developing global algorithms for recognizing and quantitative mapping of (harmful) algal blooms is questionable. On the other hand some authors cited in the present paper have found particular cases where satellites with coarse spectral and spatial resolution can be used to recognize phytoplankton blooms even at species level. Thus, the algorithms and methods to be used depend on the optical complexity of the water to which they will be applied. The aim of this paper is to summarize different methods and algorithms available in an attempt to assist in selecting the most appropriate method for a particular site and problem under investigation.