Nuisance growths of aquatic plants in Canadian surface waters continue to be problematic. Only diquat, a contact herbicide that is used to control many free-floating plants (but is less effective at controlling emergent plants), is registered in Canada for general aquatic use. Other herbicides are currently only permitted under “emergency registration.” Recent emergency registrations have been granted to glyphosate and imazapyr, and these two herbicides are likely candidates to be proposed for full registration for direct application to water in Canada in the foreseeable future. These herbicides have been extensively studied in laboratory conditions and have provided a benchmark for ecotoxicity for a variety of aquatic organisms, yet the inherent toxicity of these herbicides derived from tests does not always translate into their environmental toxicity in natural aquatic ecosystems as the fate (e.g., removal from the water body via binding to sediments and suspended solids, degradation, volatization, etc.) and exposure (i.e., continuous in the laboratory versus “pulsed” in the field) of herbicides in the natural environment is very different from their fate and exposure in laboratories. These differences will likely result in field studies having lower biological effects than laboratory studies, even if the initial exposure concentrations were similar. This review details the current knowledge based on field studies that examine the effects of the direct application of diquat, glyphosate, and imazapyr to aquatic environments on aquatic organisms. The studies of the effects of the aquatic formulations of diquat, glyphosate, and imazapyr that are reviewed here generally found negligible or short-lived impacts on fish and aquatic invertebrates in situ, whereas they found that the application of these herbicides was often beneficial through the physical modification of available habitat (i.e., an increase in open water outweighs any potential toxic effects). Conversely, certain surfactants used to increase herbicide efficacy have been suggested to be more toxic than the herbicide itself. We thus suggest monitoring the effects associated with controlled applications of diquat and other aquatic herbicides including glyphosate and imazapyr and their surfactants, as this would be a means of accumulating information that may guide future uses of herbicides in Canadian waterways.