In this article an attempt has been made to know the consequences of organic matter added in the soil-plant system for agriculture with special reference to heavy metal availability and toxicity. In the way the characteristic features of soil-heavy metal from organic matters association was described along with availability. Root absorption, transportation and accumulation in food and other plant parts are also been elaborated. Characteristics of manure, compost and vermicompost are also depicted and the fate of heavy metals in soil-plant system was mentioned. Again, some suggestions were mentioned to improve the conditions by agronomic methods such as addition of biochar, biofilm biofertilizer. Heavy metal health risk was taken in consideration in organic farming.