Rivers and estuaries are among the main entrances of litter to the marine environment. This study characterizes marine litter deposits in three estuaries of the Gulf of Biscay, assesses its potential impact in estuarine habitats based on expert elucidation, and develops a methodology to estimate the associated environmental risk. Litter was ubiquitous in the estuaries of study, mostly represented by plastic debris and sanitary waste. High marsh communities acted as litter traps, showing significantly higher litter densities than adjacent habitats. The expected impact was valued to be low but different across habitats and possible litter-habitat interactions. The estimated risk was low but different across habitats and estuaries, determined by the probability of encounter and the expected impact. This study contributes to increase the scarce knowledge available on the threat that marine litter poses in estuarine environments and presents a methodology to help identify those habitats under a higher risk.