The Water Resources Authority says it is currently conducting Dye Tracing exercises in the Rio Bueno Watershed in Trelawny.
The dyes were injected in the Quashie River near Freeman's Hall and in the Lowe River near Wait-a-Bit in the parish on Wednesday.
Members of the public expressed alarm after videos circulated on social media showed the water had turned red.
The project involves the insertion of a dye to trace the flow path of a river.
The Water Resources Authority says the dye being used is non-toxic and will dissipate in the next few days.