Over the past 15 years, significant research efforts have been channeled into assessing the effects of organic herbicides on freshwater phototrophic microbial communities. The results of this research are reviewed herein. The main conclusions we have reached after performing this review can be summarized into five points: · Most relevant assessments have dealt with the effects of triazine and phenylurea herbicides. Herbicides from these chemical classes are often considered to be model compounds when photosystem-II inhibitors are studied. · Until the early 2000s, the vast majority of investigations conducted to evaluate herbicide effects on phototropic microbes were performed in microcosms or mesocosms. In such studies, herbicides were usually applied alone, and often at concentrations much higher than those detected in the environment. More recently, the trend has been toward more realistic and relevant studies, in which lower herbicide concentrations were considered, and compound mixtures or successive treatments were tested. Increasingly, in situ studies are being designed to directly evaluate microbial community responses, following chemical exposures in contaminated aquatic environments. · Several biological end points are used to evaluate how organisms in the phototrophic microbial community respond to herbicide exposure. These end points allow the detection of quantitative changes, such as chl a concentrations, total cell counts or periphytic biomass, qualitative changes such as community structure to algal diversity, or functional changes such as photosynthesis and respiration, among others. They may give different and complementary information concerning the responses of microbial communities. · PICT approaches, which have generally combined functional and structural measurements, may prove to be valuable for assessing both an immediate impact, and for factoring in the contamination history of an ecosystem at the community level. · Finally, any relevant assessment of pesticide effects should incorporate a detailed environmental characterization that would include abiotic parameters (light, flow speed, nutrient content), or biotic parameters (diversity and structure of biofilms), because these control the bioavailability of pesticides, and thereby the exposure of microbial communities. To improve the value of ecotoxicological risk assessments, future research is needed in two key areas: first, more information on the effects of pollutants at the community level must be obtained (new tools and new end points), and second, more effort must be directed to reinforce the ecological relevance of toxicological investigations.