What were the main features of Harappan religion?

The religious beliefs of the Harappan civilization is a matter of debate and speculation due to the sparsity of evidence and a lack of interpretation of the Indus valley alphabet. 

But due to evidences unearthed so far, the following main features of Harappan religion have been confirmed:

• Worship of the Mother Goddess
• Worship of a male deity, most likely to be of Lord Shiva;
• Worship of animals, nature, semi human, or fabulous
• Worship of trees in their natural state or of their indwelling spirits
• Worship of inanimate stones or other objects, of linga and yoni symbol

For further reading check the following articles:

• Prehistoric Age in India
• Indus Valley Civilization
• Prehistoric Rock Painting