Infestation of interior walls of buildings with fungal mould is a reason for health concern which is exacerbated in energy-efficient buildings that limit air circulation. Both mycological and mycotoxicological studies are needed to determine the potential health hazards to residents. In this paper, a rare case of the occurrence of Stachybotrys chartarum in an apartment building in the Lubuskie Province in Poland has been described. Isolated as the major constituent of a mixed mycobiota, its specific health relevance still needs to be carefully analyzed as its biochemical aptitude for the synthesis of mycotoxins may be expressed at different levels. Therefore, ecotoxicological tests were performed using two bioindicators: Dugesia tigrina Girard and Daphnia magna Straus. D. tigrina was used for the first time to examine the toxicity of S. chartarum. The ecotoxicological tests showed that the analyzed strain belonged to the third and fourth toxicity classes according to Liebmann’s classification. The strain of S. chartarum was moderately toxic on Potato Dextrose Agar (PDA) as a culture medium (toxicity class III), and slightly toxic on Malt Extract Agar (MEA) (toxicity class IV). Toxicity was additionally tested by instrumental analytical methods (LC-MS/MS). This method allowed for the identification of 13 metabolites (five metabolites reported for Stachybotrys and eight for unspecific metabolites). Spirocyclic drimanes were detected in considerable quantities (ng/g); a higher concentration was observed for stachybotryamide (109,000 on PDA and 62,500 on MEA) and lower for stachybotrylactam (27,100 on PDA and 46,300 on MEA). Both may explain the result observed through the bioindicators. Highly toxic compounds such as satratoxins were not found in the sample. This confirms the applicability of the two bioindicators, which also show mutual compatibility, as suitable tools to assess the toxicity of moulds.