We derive statistical properties of standard methods for monitoring of habitat cover worldwide, and criticize them in the context of mandated seagrass monitoring programs, as exemplified by Posidonia oceanica in the Mediterranean Sea. We report the novel result that cartographic methods with non-trivial classification errors are generally incapable of reliably detecting habitat cover losses less than about 30 to 50%, and the field labor required to increase their precision can be orders of magnitude higher than that required to estimate habitat loss directly in a field campaign. We derive a universal utility threshold of classification error in habitat maps that represents the minimum habitat map accuracy above which direct methods are superior. Widespread government reliance on blind-sentinel methods for monitoring seafloor can obscure the gradual and currently ongoing losses of benthic resources until the time has long passed for meaningful management intervention. We find two classes of methods with very high statistical power for detecting small habitat cover losses: 1) fixed-plot direct methods, which are over 100 times as efficient as direct random-plot methods in a variable habitat mosaic; and 2) remote methods with very low classification error such as geospatial underwater videography, which is an emerging, low-cost, non-destructive method for documenting small changes at millimeter visual resolution. General adoption of these methods and their further development will require a fundamental cultural change in conservation and management bodies towards the recognition and promotion of requirements of minimal statistical power and precision in the development of international goals for monitoring these valuable resources and the ecological services they provide.