Heavy metal ions (e.g. cadmium, chromium, copper, nickel, arsenic, lead, zinc) have significantly serious side effects on the human health. They can bind with proteins and enzymes, altering their activity, increasing neurotoxicity, generating reactive oxygen species (ROS), promote cellular stress and resulting in their damage. Furthermore, the size, shape and type of metal are important for considering nano- or microtoxicity. It then becomes clear that the levels of these metals in drinking water are an important issue. Herein, a new micro-mechanical sensor is proposed to detect and measure these hazardous metals. The sensor consists of a micro-beam inside a micro-container. The surface of the beam is coated with a specific protein that may bind heavy metals. The mass adsorbed is measured using the resonant frequency shift of the micro-beam. This frequency shift due to the admissible mass (which is considered acceptable for drinking water based on the World Health Organization (WHO) standard) of manganese (Mn), lead (Pb), copper (Cu) and cadmium (Cd) is investigated for the first, second and third mode, respectively. Additionally, the effects of micro-beam off-center positions inside the micro-container and the mass location are investigated.