The causes of Cahokia’s collapse are less well understood than its emergence owing to the fewer settlement data available to archaeologists. Clearly, there were significant social changes that, minimally, included the abandonment of a whole upland farming district and the increased factionalization of the remaining floodplain community. Some feel that climate change and the localized deterioration of the environment may have led directly to political collapse. Certainly, there were two long dry spells “around AD 1200…back-to-back, each lasting 25 years” that brought the warmer and moist Medieval Warm Period to a close (Ollendorf 1993:175)….”
Whatever combination of factors was involved, the initial step in the process of Cahokian collapse was fundamentally a political one, The increasingly top-heavy economy the monument-laden spaces of Cahokia grew out of proportion to the shrinking farming population. The presumed results, factionalism …provided the context for the second step in the process of collapse. The first step involved domestic groups who had assumed administrative responsibilities that they had not possessed earlier. Their larger houses and multiple-building and pit household clusters-all oriented toward local pyramids or landmarks- probably correlated with larger households and greater house hold level management of domestic stores.[The second step in collapse was very abrupt.] To all intents and purposes, most Mississippians appear to have left the region permanently during the second half of the thirteenth century, and the first few decades of the fourteenth. ..By the end of the thirteenth century, when the fortified centers and their support settlements around the Ohio-Mississippi river confluence were also abandoned, the balkanization of the Mississippian world was complete.
Timothy R. Pauketat Ancient Cahokia and the Mississippians
However, it does need to be understood that while Cahokia was by far the largest grouping within that culture, not all temple-system city states collapsed when it did. Some of the groups further south survived. In fact one group ambushed Hernando de Soto (see footnote 15+ on link) in 1540 in Alabama and nearly did him in.