In this work, a procedure for the sensitive and selective determination of chlorhexidine in sludge from municipal sewage treatment plants (STPs) based on matrix solid-phase dispersion (MSPD) and liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) was optimized and validated. Analysis of sewage sludge samples, obtained from different STPs in Northwest Spain from 2018 to 2021, showed that chlorhexidine was ubiquitous in this environmental compartment with concentrations between 0.3 and 16 µg g−1. The toxicity of this pollutant was assessed in in vitro assays considering three different model organisms: Candida albicans, Escherichia coli, and Staphylococcus aureus. C. albicans was the most sensitive of the tested microorganisms to chlorhexidine with a lethal threshold concentration of 0.1 mg L−1. Thus, the lowest observed sludge residue was 3 times higher than the acute toxicity threshold measured for C. albicans. Moreover, E. coli and S. aureus were also affected at chlorhexidine concentrations around 1.8 mg L−1 and 0.5 mg L−1, respectively. So, chlorhexidine residues might affect the population of microorganisms existing in STPs. In addition, the potential phytotoxicity of the compound was evaluated with germination experiments using different model seeds. At the evaluated dose (10 µg g−1 dried soil), chlorhexidine did not affect the germination of Sorghum saccharatum, Lepidium sativum, or Sinapis alba seeds. Thus, amending agriculture soils with chlorhexidine containing sludge is unlikely to affect the germination of plants.