Display omitted •The water footprint related to food loss and waste is quantified.•The logarithmic mean Divisia index is applied to decompose the change in the water footprint.•The case of Lithuania shows that cereal crops pushed the green and grey water footprints up.•Changes in area sown and yields were important for grey, green, and blue water footprints.•Changes in the crop-mix and loss rate did not offset other factors. Food production has significant impacts on the environment, particularly in terms of water usage. Losing food along the supply chain means that all resources, including water, used to produce that food are wasted. Through the lens of the water footprint, this paper expands the scope of water resource assessment by looking at the blue, green, and grey water footprints associated with food losses along the supply chain. The index decomposition analysis (IDA) is applied to quantitatively analyze the effect of four driving factors (total area sown, crop-mix, yield, and food loss rate) to water resources related to food losses along the agri-food chain in Lithuania for the period 2003–2021. The analysis only considers food crop products meant specifically for human consumption. The results indicate an increase in the water footprint associated with food losses along the supply chain, rising from 100.5 million m3 to 131.2 million m3. This represents a 30.6% increase over the period 2003–2021, equivalent to an average annual increase of 2.6%. The total agricultural area sown under crops and yields emerge as the most significant factors shaping this increase. These effects were partially offset by changes in the crop-mix and reduced loss and waste rates.