Metal and metalloid contamination in the waterbodies and its undesirable effect on the residing diatom communities is a problem of global concern. In the present study, the effect of metals (Fe and Zn) and metalloids (As and Hg) was examined (for 15 days) in the motility and protoplasmic content of different live diatom genera under laboratory conditions. Under Hg treatment, the % motile frustules in the six diatom genera lies between 2–5% after one day of exposure, while under As treatment value lies between 30–80%. In contrast, under Zn treatment % motile frustules in the six diatom genera lie between 60–80% after one day of exposure, while under Fe treatment value lies between 40–80%. However, after 15 days of exposure to Hg, the % motile frustules in the six diatom genera lies between 0–3%, while under As treatment value lies between 5–20%. In contrast, under Zn treatment % of motile frustules in the six diatom genera lies between 10–40% after one day of exposure, while under Fe treatment value lies between 10–20%. Based on the above results, the toxicity trends of metals and metalloids showed the following: Hg > As > Fe > Zn. Based on correlation ship analysis, it is found that % motile frustules in different diatom genera showed an inverse relationship with the % reduction in the protoplasmic content of the live cells i.e., the higher the value of the reduction in protoplasmic content lower will be the % motile frustules in the community. Based on obtained results, we can conclude that motility in live diatoms is the highly sensitive endpoint to assess the impact of metal and metalloid contamination in the water bodies. However, in comparison to metals, diatoms are more sensitive to the metalloid’s exposure, especially for Hg. Finally, we conclude that % motile diatom frustules in the community is a highly sensitive, quick, and easy-to-assess biomonitoring tool for assessing the metal and metalloid contamination in the water bodies.