Although the mussel Mytilus galloprovincialis has been known for decades as an excellent bioindicator of trace element pollution in the marine environment, there is still no information on the effects of a suite of its principal morphometric parameters and age on trace element levels in soft tissues. In this work, using inductively coupled plasma mass spectrometry, we studied the contents of 72 elements in soft tissues of M. galloprovincialis aged 0.5–4, which were sampled at three stations within a relatively small water body, Sevastopol Bay. Significant effects of age and sampling location on the element contents and soft tissue dry-to-wet weight ratio were discovered. The effects of sex were not significant. It was presumed for the first time that the decrease in element content in the soft tissues of young mussels can be associated with the decrease in physiological needs for elevated contents of essential elements and intracellular water with age. Combinations of six principal morphometric parameters showed that a function of as few as three parameters (soft tissue dry weight, whole mollusk weight, and shell height, with by far the greatest contribution of the dry-to-total weight ratio) formed significant correlations with the contents of the largest possible number of elements (69–88% of the total number). For the first time, it was shown that linear discriminant analysis and canonical analysis of principal coordinates can be successfully used for tracing the exact origin of mussel samples within such a small water area. Canonical analysis of principal coordinates proved superior in the correct classification of the samples.