Although the relations between climate and settlement are not straightforward, there is a general agreement that arid conditions are less favorable for human settlement in the semiarid Near East than humid conditions. Here we show that humid conditions resulted in the abandonment of settlements along the Israeli coastal plain. We first present archaeological evidence for a drastic decline in settlement along the Israeli coast during most of the third millennium BC (Early Bronze Age II–III). Then, based on archaeological and climatic evidence, we link this decline to an environmental change occurring at that time. We propose that increased precipitation intensified the already existing drainage problems and resulted in flooding, which led to the transformation of arable land into marshes and to the spread of diseases, gradually causing settlement decline and abandonment.