Lens culinaris is a commonly grown food crop in many parts of the world however it is sensitive to waterlogging which can result in large yield losses. Waterlogging leads to root anoxia but also increased canopy humidity, therefore waterlogging stress can be compounded by foliar disease. When screening cultivars for waterlogging tolerance, previous studies have found that symptoms due to waterlogging and disease are difficult to separate. An experiment was devised to address this issue, which included 20 cultivars of lentils, both waterlogging and high relative humidity treatments, and plots with and without fungicide. Plants were grown in field soil within troughs which enabled the water level to be controlled to simulate waterlogging conditions. The 2 week waterlogging treatment was followed by a 7 week recovery period before harvest. The 2 week humidity treatment was simulated with a mister to keep the canopy moist, whilst not leading to root anoxia. Waterlogging significantly reduced plant height to between 53 and 88% of control, and reduced dry matter to between 13 and 33% of controls. It was also found that the waterlogging treatment increased prevalence, variety and severity of fungal disease in addition to reducing greenness. The two most prevalent fungi in the waterlogging treatment were Alternaria alternata and Stemphylium botryosum, identified through culturing and subsequent sequencing of the ITS region. S. botryosum was more commonly associated with disease-like symptoms and is implicated as a potential causal agent or aggravator of waterlogging symptoms. While we expected that common lentil pathogens Ascochyta lentis, Botrytis fabae and Botrytis cinerea may be present, these were not detected. Increased canopy humidity (without waterlogging) did not increase disease incidence. Tolerance to waterlogging was identified in the lentil lines Bolt, Nipper, Matador and Indianhead with reasonable root and shoot regrowth after waterlogging.