The invention provides methods and compositions for utilizing encapsulated tracer dyes in difficult liquids such as wastewater or with highly reactive treatment chemicals such as aluminum-based coagulants. In difficult liquids or highly reactive treatment chemicals even so-called “inert” tracers end up reacting and their fluorescence changes. As a result they are inconsistent and cannot be used to measure the amount of treatment chemical present. But by encapsulating the tracer dyes, even non inert tracer dyes become inert and they can reliably be used to measure the amount of treatment chemical present even if highly reactive or in a difficult liquid.