Due to the toxicity of fluoride and some metals, their presence in the environment should be monitored regularly and with a simple method. The aim of this work was to analyze several methods for the preparation of tissues from mollusks prior to biomonitoring measurements of fluoride and metals. Preparation of samples for analysis requires the greatest effort and application of different procedures depending on the sample type. We present sample preparation procedures for the analysis of fluoride content in mollusk shell using the ion-selective electrode and in soft tissues using gas chromatography, as well as of metals in various mollusk tissues with atomic absorption spectrometry.