The Murray Darling Basin (MDB) is Australia’s most important agricultural region. The southern MDB receives most of its annual catchment runoff during the cool season (April-September). Focusing on the Murrumbidgee River measurements at Wagga Wagga and further downstream at Hay, river heights in the cool season decreased markedly in variability over a century prior to 1991. Box and whisker plots of 27-year April-September Hay and Wagga Wagga river heights reveal decreases not matched by declining April-September catchment rainfall. However, permutation tests of both means and variances of late autumn (April-May) dam catchment rainfall and inflows, produced p-values indicating a highly significant decline since the early 1990s. Consequently, dry catchments in late autumn, even with average cool season rainfall, have reduced dam inflows and decreased river heights downstream from Wagga Wagga, before water extraction for irrigation. It is concluded that lower April-September mean river heights at Wagga Wagga and decreased river height variability at Hay, since the mid-1990s, are due to combined lesser April-May catchment rainfall and increased mean temperatures. If these drying and warming trends continue, they will drastically reduce water availability for the Murrumbidgee River catchment and, consequently, for a vital part of the southern MDB.