The functioning and sustainability of lotic ecosystems depend to a large extent on their thermal and hydrological regimes. In the Mediterranean region, these factors are very sensitive to climate and anthropization which have undergone deep changes over the last four decades. Having noted the drying up of many permanent streams in Morocco, we conducted in 2015-2017 a new study with the aim of analyzing and assessing abiotic changes in the Upper Sebou (Middle Atlas, Morocco). A former study was carried out in 1981-1985. Indeed, over the last four decades, this river has been exposed to multiple disturbances, due to both recurrent droughts and human pressures. To describe and assess these changes, we used 16 abiotic variables that were measured in 11 ecosystems along the central course of the river. The comparison was mainly carried out using the multiple factorial correspondence analysis (MFCA), through a ternary matrix “variables × stations × time”, gathering old and new data in the same mesological structure. The analysis revealed the classical upstream-downstream ordering of the studied ecosystems, where most of the ecosystems recorded a downstream migration from their 1981 position. In this evolutionary perspective, the study involves hydrological and thermal factors, which show mainly a reduction in flow and a slight increase in temperature and water mineralization, both in summer and winter. It is assumed that water withdrawals, especially for irrigation, together with climatic droughts in the region, are responsible for these long-term evolutionary trends.