Moss-bags were applied to study the effect of contamination in three standing water bodies in Bulgaria (Kardzhali, Studen Kladenets and Zhrebchevo Reservoirs), the first two with old industrial contamination and the last polluted with short-chain chlorinated paraffins (SCCPs). Fontinalis antipyretica Hedw. collected from background (unpolluted) site was placed in cages for a period of 30 days. The present study examined whether inorganic and organic pollution detected with moss-bags resulted in corresponding differences in molecular, chemical and micromorphological markers. Suppressed large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL) expression was assessed in moss-bags from two of the reservoirs, contaminated with heavy metals. There was a decrease of the total phenolic content (TPC) in the moss-bags, which provides a basis for further studies of the chemical content of aquatic mosses. Fontinalis antipyretica also showed a response through leaf micromorphological characteristics. In the all three reservoirs, an increase of the twig leaf cell number was recorded (p ≤ 0.01 for Kardzhali and p ≤ 0.001 for Studen Kladenets and Zhrebchevo reservoirs), as well as of the stem leaf cell number in Zhrebchevo Reservoir (p ≤ 0.001). On the contrary, the width of the cells decreased in the studied anthropogenically impacted reservoirs. All three studied groups of biomarkers (molecular, chemical and micromorphological) appeared to be sensitive to freshwater pollution. The results achieved indicated that rbcL gene expression, TPC, cell number and size are promising biomonitoring tools.