Cysts and (oo)cysts are the infective forms of parasitic protozoa, as Giardia and Cryptosporidium, which are widespread and associated to worldwide waterborne diseases outbreaks. These microorganisms pose a challenge to public health, as they are resistant to conventional disinfection methods, which make them important parameters when evaluating inactivation efficiency. However, when (oo)cysts are targets, it is challenging to infer inactivation efficacy, as it may require infectivity tests that are not often an option for laboratory routine analysis. In this scene, (oo)cyst viability based on induced excystation, membrane integrity and enzyme activity evaluated by dye inclusion and/or exclusion, as well as fluorescence reduction consist on microscopy-based techniques that may be options to estimate inactivation in the environmental context. This scoping review presents applications, advantages and limitations of these methodologies for viability assessment, in order to shed light on the (oo)cyst viability topic and provide insight strategies for choosing protocols in the environmental and sanitation field, in laboratory applications and novel research.