DEFRA has just published the description for 11 activities that may take place in on or near a main river or sea defence which do not require an environmental permit. This includes site investigation boreholes and trial pits that are completed and refilled within 48hours. 
To see whether your site investigation meets all of the requirements of the exclusion please go to https://www.gov.uk/government/publications/excluded-flood-risk-activities-environmental-permits/excluded-flood-risk-activities.
