This study aimed to examine spatiotemporal variations in chironomid assemblages and to detect how environmental variables affect their structure. We sampled seven streams at low and high altitudes in Northwest Argentina under contrasting climate conditions (Puna and Chaco Serrano) during high- and low-water periods. The environmental variables that affected Chironomidae community structure were water temperature, conductivity, hardness, current velocity and type of substrate. Fine substrates, gravel and low water temperature favoured cold stenothermal fauna, composed of Orthocladiinae, Diamesinae and Podonominae specimens in the high-altitude streams, whereas warm waters with low conductivity and higher velocity favoured increased species diversity in lowland streams, where there was greater abundance of Chironominae (which corresponds to warm eurythermal fauna). The studied environments belong to a transition zone that should be preserved where cold stenothermic and warm eurythermal Chironomidae overlap.