Raw wastewater analysis is an important step in treatment assessment; however, it is associated with risks of personnel exposure to pathogens. Such risks are enhanced during virus outbreaks, such as the COVID pandemic, and heat-treatment is a commonly used mitigation measure. We examined whether heat-treatment compromises wastewater analytical parameters results. We found that heat-treatment of blackwater at 60 °C for 90 min in capped containers yielded no statistically different values (p > 0.05) for pH, chemical oxygen demand (COD), ammonia (NH3), total nitrogen (TN), total suspended solids (TSS), and turbidity for specimens from three different sources. This heat-treatment inactivated coliform bacteria (>4 log10 reduction) thus compromising the measurement of commonly used fecal contamination indicators. The observation of intact helminth eggs in heat-treated specimens suggests that the helminth egg enumeration assay is not compromised. These findings indicate that heat-treatment for the safe handling of wastewater, as may be needed in future virus outbreaks, does not affect the measurements of many common wastewater physico-chemical properties.